1
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Mehrotra S, Kalyan BG P, Nayak PG, Joseph A, Manikkath J. Recent Progress in the Oral Delivery of Therapeutic Peptides and Proteins: Overview of Pharmaceutical Strategies to Overcome Absorption Hurdles. Adv Pharm Bull 2024; 14:11-33. [PMID: 38585454 PMCID: PMC10997937 DOI: 10.34172/apb.2024.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 07/04/2023] [Accepted: 08/16/2023] [Indexed: 04/09/2024] Open
Abstract
Purpose Proteins and peptides have secured a place as excellent therapeutic moieties on account of their high selectivity and efficacy. However due to oral absorption limitations, current formulations are mostly delivered parenterally. Oral delivery of peptides and proteins (PPs) can be considered the need of the hour due to the immense benefits of this route. This review aims to critically examine and summarize the innovations and mechanisms involved in oral delivery of peptide and protein drugs. Methods Comprehensive literature search was undertaken, spanning the early development to the current state of the art, using online search tools (PubMed, Google Scholar, ScienceDirect and Scopus). Results Research in oral delivery of proteins and peptides has a rich history and the development of biologics has encouraged additional research effort in recent decades. Enzyme hydrolysis and inadequate permeation into intestinal mucosa are the major causes that result in limited oral absorption of biologics. Pharmaceutical and technological strategies including use of absorption enhancers, enzyme inhibition, chemical modification (PEGylation, pro-drug approach, peptidomimetics, glycosylation), particulate delivery (polymeric nanoparticles, liposomes, micelles, microspheres), site-specific delivery in the gastrointestinal tract (GIT), membrane transporters, novel approaches (self-nanoemulsifying drug delivery systems, Eligen technology, Peptelligence, self-assembling bubble carrier approach, luminal unfolding microneedle injector, microneedles) and lymphatic targeting, are discussed. Limitations of these strategies and possible innovations for improving oral bioavailability of protein and peptide drugs are discussed. Conclusion This review underlines the application of oral route for peptide and protein delivery, which can direct the formulation scientist for better exploitation of this route.
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Affiliation(s)
- Sonal Mehrotra
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Pavan Kalyan BG
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | - Pawan Ganesh Nayak
- Department of Pharmacology,Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
| | | | - Jyothsna Manikkath
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka State, India
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2
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Wu M, Huang W, Yang N, Liu Y. Learn from antibody–drug conjugates: consideration in the future construction of peptide-drug conjugates for cancer therapy. Exp Hematol Oncol 2022; 11:93. [DOI: 10.1186/s40164-022-00347-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractCancer is one of the leading causes of death worldwide due to high heterogeneity. Although chemotherapy remains the mainstay of cancer therapy, non-selective toxicity and drug resistance of mono-chemotherapy incur broad criticisms. Subsequently, various combination strategies have been developed to improve clinical efficacy, also known as cocktail therapy. However, conventional “cocktail administration” is just passable, due to the potential toxicities to normal tissues and unsatisfactory synergistic effects, especially for the combined drugs with different pharmacokinetic properties. The drug conjugates through coupling the conventional chemotherapeutics to a carrier (such as antibody and peptide) provide an alternative strategy to improve therapeutic efficacy and simultaneously reduce the unspecific toxicities, by virtue of the advantages of highly specific targeting ability and potent killing effect. Although 14 antibody–drug conjugates (ADCs) have been approved worldwide and more are being investigated in clinical trials so far, several limitations have been disclosed during clinical application. Compared with ADCs, peptide-drug conjugates (PDCs) possess several advantages, including easy industrial synthesis, low cost, high tissue penetration and fast clearance. So far, only a handful of PDCs have been approved, highlighting tremendous development potential. Herein, we discuss the progress and pitfalls in the development of ADCs and underline what can learn from ADCs for the better construction of PDCs in the future.
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3
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Anticancer peptides mechanisms, simple and complex. Chem Biol Interact 2022; 368:110194. [PMID: 36195187 DOI: 10.1016/j.cbi.2022.110194] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022]
Abstract
Peptide therapy has started since 1920s with the advent of insulin application, and now it has emerged as a new approach in treatment of diseases including cancer. Using anti-cancer peptides (ACPs) is a promising way of cancer therapy as ACPs are continuing to be approved and arrived at major pharmaceutical markets. Traditional cancer treatments face different problems like intensive adverse effects to patient's body, cell resistance to conventional chemical drugs and in some worse cases the occurrence of cell multidrug resistance (MDR) of cancerous tissues against chemotherapy. On the other hand, there are some benefits conceived for peptides usage in treatment of diseases specifically cancer, as these compounds present favorable characteristics such as smaller size, high activity, low immunogenicity, good biocompatibility in vivo, convenient and rapid way of synthesis, amenable to sequence modification and revision and there is no limitation for the type of cargo they carry. It is possible to achieve an optimum molecular and functional structure of peptides based on previous experience and bank of peptide motif data which may result in novel peptide design. Bioactive peptides are able to form pores in cell membrane and induce necrosis or apoptosis of abnormal cells. Moreover, recent researches have focused on the tumor recognizing peptide motifs with the ability to permeate to cancerous cells with the aim of cancer treatment at earlier stages. In this strategy the most important factors for addressing cancer are choosing peptides with easy accessibility to tumor cell without cytotoxicity effect towards normal cells. The peptides must also meet acceptable pharmacokinetic requirements. In this review, the characteristics of peptides and cancer cells are discussed. The various mechanisms of peptides' action proposed against cancer cells make the next part of discussion. It will be followed by giving information on peptides application, various methods of peptide designing along with introducing various databases. Future aspects of peptides for employing in area of cancer treatment come as conclusion at the end.
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4
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Optimized peptide extraction method for analysis of antimicrobial peptide Kn2-7/dKn2-7 stability in human serum by LC-MS. Future Sci OA 2022; 8:FSO807. [PMID: 35909998 PMCID: PMC9327644 DOI: 10.2144/fsoa-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Aim: To develop an extraction protocol and determine stability for antimicrobial peptide (AMP) Kn2-7 and its d-enantiomer dKn2-7 in human serum. Materials & methods: We compared use of ethanol, acetonitrile, RapiGest SF Surfactant and 1% formic acid in ethanol for AMP recovery from serum prior to liquid chromatography-mass spectrometry quantification. Results: Precipitation of samples with 1% formic acid in ethanol caused the least amount of AMP loss during extraction from serum. Time-course experiments revealed dKn2-7 was significantly more stable than Kn2-7 in 25% serum, with 78.5% of dKn2-7 and only 1.0% of Kn2-7 remaining after 24 h at 37°C. Conclusion: The optimized method significantly increased peptide recovery and allowed more accurate and consistent quantification of Kn2-7 and dKn2-7 serum stability. Antimicrobial peptides are a new class of molecules being studied for treatment of infections. These peptides can easily be broken down by enzymes present in the body. Removal of the peptides by the enzymes might limit the effect of the drugs against an infection. Our work discusses the importance of testing the stability of these peptides in human serum, a bodily fluid that contains a large amount of enzymes. We describe a method to decrease loss of two potential peptide drugs during sample processing. Further, we report results of testing the stability of these two peptide drugs in human serum. Peptide extraction was optimized for maximum recovery of antimicrobial peptides Kn2-7/dKn2-7 from serum for LC–MS analysis. Time course experiments revealed d-amino acid analogue antimicrobial peptides were more stable against host proteases.
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5
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Koch P, Schmitt S, Cardner M, Beerenwinkel N, Panke S, Held M. Discovery of antimicrobials by massively parallelized growth assays (Me x). Sci Rep 2022; 12:4097. [PMID: 35260685 PMCID: PMC8904554 DOI: 10.1038/s41598-022-07755-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/17/2022] [Indexed: 01/12/2023] Open
Abstract
The number of newly approved antimicrobial compounds has been steadily decreasing over the past 50 years emphasizing the need for novel antimicrobial substances. Here we present Mex, a method for the high-throughput discovery of novel antimicrobials, that relies on E. coli self-screening to determine the bioactivity of more than ten thousand naturally occurring peptides. Analysis of thousands of E. coli growth curves using next-generation sequencing enables the identification of more than 1000 previously unknown antimicrobial peptides. Additionally, by incorporating the kinetics of growth inhibition, a first indication of the mode of action is obtained, which has implications for the ultimate usefulness of the peptides in question. The most promising peptides of the screen are chemically synthesized and their activity is determined in standardized susceptibility assays. Ten out of 15 investigated peptides efficiently eradicate bacteria at a minimal inhibitory concentration in the lower µM or upper nM range. This work represents a step-change in the high-throughput discovery of functionally diverse antimicrobials.
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Affiliation(s)
- Philipp Koch
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Steven Schmitt
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Mathias Cardner
- Computational Biology, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Niko Beerenwinkel
- Computational Biology, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Sven Panke
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Held
- Bioprocess Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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Düzgüneş N, Fernandez-Fuentes N, Konopka K. Inhibition of Viral Membrane Fusion by Peptides and Approaches to Peptide Design. Pathogens 2021; 10:1599. [PMID: 34959554 PMCID: PMC8709411 DOI: 10.3390/pathogens10121599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Fusion of lipid-enveloped viruses with the cellular plasma membrane or the endosome membrane is mediated by viral envelope proteins that undergo large conformational changes following binding to receptors. The HIV-1 fusion protein gp41 undergoes a transition into a "six-helix bundle" after binding of the surface protein gp120 to the CD4 receptor and a co-receptor. Synthetic peptides that mimic part of this structure interfere with the formation of the helix structure and inhibit membrane fusion. This approach also works with the S spike protein of SARS-CoV-2. Here we review the peptide inhibitors of membrane fusion involved in infection by influenza virus, HIV-1, MERS and SARS coronaviruses, hepatitis viruses, paramyxoviruses, flaviviruses, herpesviruses and filoviruses. We also describe recent computational methods used for the identification of peptide sequences that can interact strongly with protein interfaces, with special emphasis on SARS-CoV-2, using the PePI-Covid19 database.
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Affiliation(s)
- Nejat Düzgüneş
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, UK;
| | - Krystyna Konopka
- Department of Biomedical Sciences, Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, CA 94103, USA;
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7
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Target identification for small-molecule discovery in the FOXO3a tumor-suppressor pathway using a biodiverse peptide library. Cell Chem Biol 2021; 28:1602-1615.e9. [PMID: 34111400 PMCID: PMC8610377 DOI: 10.1016/j.chembiol.2021.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/03/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022]
Abstract
Genetic screening technologies to identify and validate macromolecular interactions (MMIs) essential for complex pathways remain an important unmet need for systems biology and therapeutics development. Here, we use a library of peptides from diverse prokaryal genomes to screen MMIs promoting the nuclear relocalization of Forkhead Box O3 (FOXO3a), a tumor suppressor more frequently inactivated by post-translational modification than mutation. A hit peptide engages the 14-3-3 family of signal regulators through a phosphorylation-dependent interaction, modulates FOXO3a-mediated transcription, and suppresses cancer cell growth. In a crystal structure, the hit peptide occupies the phosphopeptide-binding groove of 14-3-3ε in a conformation distinct from its natural peptide substrates. A biophysical screen identifies drug-like small molecules that displace the hit peptide from 14-3-3ε, providing starting points for structure-guided development. Our findings exemplify “protein interference,” an approach using evolutionarily diverse, natural peptides to rapidly identify, validate, and develop chemical probes against MMIs essential for complex cellular phenotypes. We describe protein interference, an approach to identify and validate new drug targets A genetic screen identifies a protein interference probe inducing FOXO3a reactivation The probe defines a druggable binding site in the 14-3-3 signal regulator family We illustrate a workflow to parse complex cellular pathways for new drug targets
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8
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Wang J, Miao Y. Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding. J Chem Phys 2021; 153:154109. [PMID: 33092378 DOI: 10.1063/5.0021399] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Peptides mediate up to 40% of known protein-protein interactions in higher eukaryotes and play an important role in cellular signaling. However, it is challenging to simulate both binding and unbinding of peptides and calculate peptide binding free energies through conventional molecular dynamics, due to long biological timescales and extremely high flexibility of the peptides. Based on the Gaussian accelerated molecular dynamics (GaMD) enhanced sampling technique, we have developed a new computational method "Pep-GaMD," which selectively boosts essential potential energy of the peptide in order to effectively model its high flexibility. In addition, another boost potential is applied to the remaining potential energy of the entire system in a dual-boost algorithm. Pep-GaMD has been demonstrated on binding of three model peptides to the SH3 domains. Independent 1 µs dual-boost Pep-GaMD simulations have captured repetitive peptide dissociation and binding events, which enable us to calculate peptide binding thermodynamics and kinetics. The calculated binding free energies and kinetic rate constants agreed very well with available experimental data. Furthermore, the all-atom Pep-GaMD simulations have provided important insights into the mechanism of peptide binding to proteins that involves long-range electrostatic interactions and mainly conformational selection. In summary, Pep-GaMD provides a highly efficient, easy-to-use approach for unconstrained enhanced sampling and calculations of peptide binding free energies and kinetics.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, USA
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9
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Huang W, Soeung V, Boragine DM, Palzkill T. Mapping Protein-Protein Interaction Interface Peptides with Jun-Fos Assisted Phage Display and Deep Sequencing. ACS Synth Biol 2020; 9:1882-1896. [PMID: 32502338 DOI: 10.1021/acssynbio.0c00242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions govern many cellular processes, and identifying binding interaction sites on proteins can facilitate the discovery of inhibitors to block such interactions. Here we identify peptides from a randomly fragmented plasmid encoding the β-lactamase inhibitory protein (BLIP) and the Lac repressor (LacI) that represent regions of protein-protein interactions. We utilized a Jun-Fos-assisted phage display system that has previously been used to screen cDNA and genomic libraries to identify antibody antigens. Affinity selection with polyclonal antibodies against LacI or BLIP resulted in the rapid enrichment of in-frame peptides from various regions of the proteins. Further, affinity selection with β-lactamase enriched peptides that encompass regions of BLIP previously shown to contribute strongly to the binding energy of the BLIP/β-lactamase interaction, i.e., hotspot residues. Further, one of the regions enriched by affinity selection encompassed a disulfide-constrained region of BLIP that forms part of the BLIP interaction surface in the native complex that we show also binds to β-lactamase as a disulfide-constrained macrocycle peptide with a KD of ∼1 μM. Fragmented open reading frame (ORF) libraries may efficiently identify such naturally constrained peptides at protein-protein interaction interfaces. With sufficiently deep coverage of ORFs by peptide-coding inserts, phage display and deep sequencing can provide detailed information on the domains or peptides that contribute to an interaction. Such information should enable the design of potentially therapeutic macrocycles or peptidomimetics that block the interaction.
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10
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Alavi SE, Cabot PJ, Moyle PM. Glucagon-Like Peptide-1 Receptor Agonists and Strategies To Improve Their Efficiency. Mol Pharm 2019; 16:2278-2295. [PMID: 31050435 DOI: 10.1021/acs.molpharmaceut.9b00308] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is increasing in global prevalence and is associated with serious health problems (e.g., cardiovascular disease). Various treatment options are available for T2DM, including the incretin hormone glucagon-like peptide-1 (GLP-1). GLP-1 is a therapeutic peptide secreted from the intestines following food intake, which stimulates the secretion of insulin from the pancreas. The native GLP-1 has a very short plasma half-life, owning to renal clearance and degradation by the enzyme dipeptidyl peptidase-4. To overcome this issue, various GLP-1 agonists with increased resistance to proteolytic degradation and reduced renal clearance have been developed, with several currently marketed. Strategies, such as controlled release delivery systems, methods to reduce renal clearance (e.g., PEGylation and conjugation to antibodies), and methods to improve proteolytic stability (e.g., stapling, cyclization, and glycosylation) provide means to further improve the ability of GLP-1 analogs. These will be discussed in this literature review.
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Affiliation(s)
- Seyed Ebrahim Alavi
- School of Pharmacy , The University of Queensland , Woolloongabba , 4102 , Australia
| | - Peter J Cabot
- School of Pharmacy , The University of Queensland , Woolloongabba , 4102 , Australia
| | - Peter M Moyle
- School of Pharmacy , The University of Queensland , Woolloongabba , 4102 , Australia
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11
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Abstract
The implication of several TRP ion channels (e.g., TRPV1) in diverse physiological and pathological processes has signaled them as pivotal drug targets. Consequently, the identification of selective and potent ligands for these channels is of great interest in pharmacology and biomedicine. However, a major challenge in the design of modulators is ensuring the specificity for their intended targets. In recent years, the emergence of high-resolution structures of ion channels facilitates the computer-assisted drug design at molecular levels. Here we describe some computational methods and general protocols to discover channel modulators, including homology modelling, docking and virtual screening, and structure-based peptide design.
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Affiliation(s)
- Magdalena Nikolaeva Koleva
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universitas Miguel Hernández, Elche, Spain
- AntalGenics SL. Ed. Quorum III, University Scientific Park, Universitas Miguel Hernández, Elche, Spain
| | - Gregorio Fernandez-Ballester
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universitas Miguel Hernández, Elche, Spain.
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12
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A platform for discovery of functional cell-penetrating peptides for efficient multi-cargo intracellular delivery. Sci Rep 2018; 8:12538. [PMID: 30135446 PMCID: PMC6105642 DOI: 10.1038/s41598-018-30790-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022] Open
Abstract
Cell penetrating peptides (CPPs) offer great potential to deliver therapeutic molecules to previously inaccessible intracellular targets. However, many CPPs are inefficient and often leave their attached cargo stranded in the cell’s endosome. We report a versatile platform for the isolation of peptides delivering a wide range of cargos into the cytoplasm of cells. We used this screening platform to identify multiple “Phylomer” CPPs, derived from bacterial and viral genomes. These peptides are amenable to conventional sequence optimization and engineering approaches for cell targeting and half-life extension. We demonstrate potent, functional delivery of protein, peptide, and nucleic acid analog cargos into cells using Phylomer CPPs. We validate in vivo activity in the cytoplasm, through successful transport of an oligonucleotide therapeutic fused to a Phylomer CPP in a disease model for Duchenne’s muscular dystrophy. This report thus establishes a discovery platform for identifying novel, functional CPPs to expand the delivery landscape of druggable intracellular targets for biological therapeutics.
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13
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Wang E, Sorolla A, Cunningham PT, Bogdawa HM, Beck S, Golden E, Dewhurst RE, Florez L, Cruickshank MN, Hoffmann K, Hopkins RM, Kim J, Woo AJ, Watt PM, Blancafort P. Tumor penetrating peptides inhibiting MYC as a potent targeted therapeutic strategy for triple-negative breast cancers. Oncogene 2018; 38:140-150. [PMID: 30076412 PMCID: PMC6318000 DOI: 10.1038/s41388-018-0421-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 05/24/2018] [Accepted: 06/29/2018] [Indexed: 12/21/2022]
Abstract
Overexpression of MYC oncogene is highly prevalent in many malignancies such as aggressive triple-negative breast cancers (TNBCs) and it is associated with very poor outcome. Despite decades of research, attempts to effectively inhibit MYC, particularly with small molecules, still remain challenging due to the featureless nature of its protein structure. Herein, we describe the engineering of the dominant-negative MYC peptide (OmoMYC) linked to a functional penetrating 'Phylomer' peptide (FPPa) as a therapeutic strategy to inhibit MYC in TNBC. We found FPPa-OmoMYC to be a potent inducer of apoptosis (with IC50 from 1-2 µM) in TNBC cells with negligible effects in non-tumorigenic cells. Transcriptome analysis of FPPa-OmoMYC-treated cells indicated that the fusion protein inhibited MYC-dependent networks, inducing dynamic changes in transcriptional, metabolic, and apoptotic processes. We demonstrated the efficacy of FPPa-OmoMYC in inhibiting breast cancer growth when injected orthotopically in TNBC allografts. Lastly, we identified strong pharmacological synergisms between FPPa-OmoMYC and chemotherapeutic agents. This study highlights a novel therapeutic approach to target highly aggressive and chemoresistant MYC-activated cancers.
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Affiliation(s)
- Edina Wang
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Anabel Sorolla
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Paula T Cunningham
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Heique M Bogdawa
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Samuel Beck
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,MDI Biological Laboratory, Kathryn W. Davis Center for Regenerative Biology and Medicine, Salisbury Cove, ME, 04672, USA
| | - Emily Golden
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Robert E Dewhurst
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Laura Florez
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | - Katrin Hoffmann
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia.,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia
| | | | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew J Woo
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Paul M Watt
- Phylogica Pty Ltd, Subiaco, WA, 6008, Australia. .,Telethon Kids Institute, The University of Western Australia, Subiaco, WA, 6008, Australia.
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia. .,School of Human Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.
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14
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Structure-diverse Phylomer libraries as a rich source of bioactive hits from phenotypic and target directed screens against intracellular proteins. Curr Opin Chem Biol 2017; 38:127-133. [DOI: 10.1016/j.cbpa.2017.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 01/15/2023]
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15
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Zebrafish as a model to evaluate peptide-related cancer therapies. Amino Acids 2017; 49:1907-1913. [DOI: 10.1007/s00726-017-2388-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/27/2017] [Indexed: 02/03/2023]
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16
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Nijnik A, Hancock REW. Host defence peptides: antimicrobial and immunomodulatory activity and potential applications for tackling antibiotic-resistant infections. EMERGING HEALTH THREATS JOURNAL 2017. [DOI: 10.3402/ehtj.v2i0.7078] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- A Nijnik
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada
| | - REW Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, Canada
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17
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Candido-Ferreira IL, Kronenberger T, Sayegh RSR, Batista IDFC, da Silva Junior PI. Evidence of an Antimicrobial Peptide Signature Encrypted in HECT E3 Ubiquitin Ligases. Front Immunol 2017; 7:664. [PMID: 28119686 PMCID: PMC5220581 DOI: 10.3389/fimmu.2016.00664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is a hallmark of the eukaryotic cell. In jawed vertebrates, it has been co-opted by the adaptive immune system, where proteasomal degradation produces endogenous peptides for major histocompatibility complex class I antigen presentation. However, proteolytic products are also necessary for the phylogenetically widespread innate immune system, as they often play a role as host defense peptides (HDPs), pivotal effectors against pathogens. Here, we report the identification of the arachnid HDP oligoventin, which shares homology to a core member of the UPP, E3 ubiquitin ligases. Oligoventin has broad antimicrobial activity and shows strong synergy with lysozymes. Using computational and phylogenetic approaches, we show high conservation of the oligoventin signature in HECT E3s. In silico simulation of HECT E3s self-proteolysis provides evidence that HDPs can be generated by fine-tuned 26S proteasomal degradation, and therefore are consistent with the hypothesis that oligoventin is a cryptic peptide released by the proteolytic processing of an Nedd4 E3 precursor protein. Finally, we compare the production of HDPs and endogenous antigens from orthologous HECT E3s by proteasomal degradation as a means of analyzing the UPP coupling to metazoan immunity. Our results highlight the functional plasticity of the UPP in innate and adaptive immune systems as a possibly recurrent mechanism to generate functionally diverse peptides.
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Affiliation(s)
- Ivan Lavander Candido-Ferreira
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, Brazil; Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo , São Paulo, São Paulo , Brazil
| | - Raphael Santa Rosa Sayegh
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, Brazil; Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Pedro Ismael da Silva Junior
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute , São Paulo, São Paulo , Brazil
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Kim S, Lee JH, Kang I, Hyun S, Yu J, Shin C. An Amphiphilic Peptide Induces Apoptosis Through the miR29b-p53 Pathway in Cancer Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e330. [PMID: 27377134 PMCID: PMC5014530 DOI: 10.1038/mtna.2016.45] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/17/2016] [Indexed: 12/18/2022]
Abstract
Peptides have been in the limelight, as therapeutic agents for cancer treatment through various applications due to their high target selectivity and exceptional ability to penetrate the cell membrane. Recent studies have revealed that synthesized peptides bind to hairpin structures of RNA that affect their activities such as changing the efficacy of microRNA maturation. MicroRNA-mediated p53 activation by the microRNA-29 (miR29) family is one of the most important regulatory pathways in cancer therapeutics. By targeting the suppressors of p53, a tumor suppressor protein, miR29 induces apoptosis of cancer cells through p53 stabilization. Here, we identify a novel synthesized amphiphilic peptide, LK-L1C/K6W/L8C, which enhances expression of miR29b and promotes p53 activity. In the presence of LK-L1C/K6W/L8C, pre-miR29b preferentially forms a complex with the Dicer protein through interaction of LK-L1C/K6W/L8C with the terminal loop region of pre-miR29b, leading to an increase in Dicer processing. Furthermore, LK-L1C/K6W/L8C stimulates apoptosis by improving p53 stability in miR29-inducible HeLa and MCF7 cells. Collectively, our study shows that a peptide can directly influence the miR29b-mediated p53 activation pathway in cancer cells. Therefore, our findings provide the basis for a new, potentially promising peptide-based drug for cancer therapy.
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Affiliation(s)
- Soyoung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jung Hyun Lee
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Igojo Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Soonsil Hyun
- Department of Chemistry and Education, Seoul National University, Seoul, Republic of Korea
| | - Jaehoon Yu
- Department of Chemistry and Education, Seoul National University, Seoul, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
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Obarska-Kosinska A, Iacoangeli A, Lepore R, Tramontano A. PepComposer: computational design of peptides binding to a given protein surface. Nucleic Acids Res 2016; 44:W522-8. [PMID: 27131789 PMCID: PMC4987918 DOI: 10.1093/nar/gkw366] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/22/2016] [Indexed: 02/03/2023] Open
Abstract
There is a wide interest in designing peptides able to bind to a specific region of a protein with the aim of interfering with a known interaction or as starting point for the design of inhibitors. Here we describe PepComposer, a new pipeline for the computational design of peptides binding to a given protein surface. PepComposer only requires the target protein structure and an approximate definition of the binding site as input. We first retrieve a set of peptide backbone scaffolds from monomeric proteins that harbor the same backbone arrangement as the binding site of the protein of interest. Next, we design optimal sequences for the identified peptide scaffolds. The method is fully automatic and available as a web server at http://biocomputing.it/pepcomposer/webserver.
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Affiliation(s)
| | - Alfredo Iacoangeli
- Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy
| | - Rosalba Lepore
- Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy
| | - Anna Tramontano
- Department of Physics, Sapienza University, Piazzale Aldo Moro, 5-00184 Rome, Italy Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
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20
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Lu MC, Yuan ZW, Jiang YL, Chen ZY, You QD, Jiang ZY. A systematic molecular dynamics approach to the study of peptide Keap1–Nrf2 protein–protein interaction inhibitors and its application to p62 peptides. MOLECULAR BIOSYSTEMS 2016; 12:1378-87. [DOI: 10.1039/c6mb00030d] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein–protein interactions (PPIs) as drug targets have been gaining growing interest, though developing drug-like small molecule PPI inhibitors remains challenging.
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Affiliation(s)
- Meng-Chen Lu
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Zhen-Wei Yuan
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Yong-Lin Jiang
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Zhi-Yun Chen
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Qi-Dong You
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
| | - Zheng-Yu Jiang
- State Key Laboratory of Natural Medicines
- China Pharmaceutical University
- Nanjing 210009
- China
- Jiangsu Key Laboratory of Drug Design and Optimization
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21
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Review cyclic peptides on a merry-go-round; towards drug design. Biopolymers 2015; 104:453-61. [DOI: 10.1002/bip.22669] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/14/2015] [Accepted: 05/04/2015] [Indexed: 01/15/2023]
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22
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Oliva B, Fernandez-Fuentes N. Knowledge-based modeling of peptides at protein interfaces: PiPreD. Bioinformatics 2014; 31:1405-10. [PMID: 25540186 DOI: 10.1093/bioinformatics/btu838] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/14/2014] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION Protein-protein interactions (PPIs) underpin virtually all cellular processes both in health and disease. Modulating the interaction between proteins by means of small (chemical) agents is therefore a promising route for future novel therapeutic interventions. In this context, peptides are gaining momentum as emerging agents for the modulation of PPIs. RESULTS We reported a novel computational, structure and knowledge-based approach to model orthosteric peptides to target PPIs: PiPreD. PiPreD relies on a precompiled and bespoken library of structural motifs, iMotifs, extracted from protein complexes and a fast structural modeling algorithm driven by the location of native chemical groups on the interface of the protein target named anchor residues. PiPreD comprehensive and systematically samples the entire interface deriving peptide conformations best suited for the given region on the protein interface. PiPreD complements the existing technologies and provides new solutions for the disruption of selected interactions. AVAILABILITY AND IMPLEMENTATION Database and accessory scripts and programs are available upon request to the authors or at http://www.bioinsilico.org/PIPRED. CONTACT narcis.fernandez@gmail.com.
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Affiliation(s)
- Baldo Oliva
- Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Narcis Fernandez-Fuentes
- Structural Bioinformatics Lab (GRIB), Departament de Ciencies Experimental i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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23
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Jefferies R, Yang R, Woh CK, Weldt T, Milech N, Estcourt A, Armstrong T, Hopkins R, Watt P, Reid S, Armson A, Ryan UM. Target validation of the inosine monophosphate dehydrogenase (IMPDH) gene in Cryptosporidium using Phylomer(®) peptides. Exp Parasitol 2014; 148:40-8. [PMID: 25447124 DOI: 10.1016/j.exppara.2014.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/07/2014] [Indexed: 01/03/2023]
Abstract
Cryptosporidiosis, a gastroenteric disease characterised mainly by diarrheal illnesses in humans and mammals is caused by infection with the protozoan parasite Cryptosporidium. Treatment options for cryptosporidiosis are limited, with the current therapeutic nitazoxanide, only partly efficacious in immunocompetent individuals. The parasite lacks de novo purine synthesis, and is exclusively dependant on purine salvage from its host. Inhibition of the inosine 5' monophosphate dehydrogenase (IMPDH), a purine salvage enzyme that is essential for DNA synthesis, thereby offers a potential drug target against this parasite. In the present study, a yeast-two-hybrid system was used to identify Phylomer peptides within a library constructed from the genomes of 25 phylogenetically diverse bacteria that targeted the IMPDH of Cryptosporidium parvum (IMPcp) and Cryptosporidium hominis (IMPch). We identified 38 unique interacting Phylomers, of which, 12 were synthesised and screened against C. parvum in vitro. Two Phylomers exhibited significant growth inhibition (81.2-83.8% inhibition; P < 0.05), one of which consistently exhibited positive interactions with IMPcp and IMPch during primary and recapitulation yeast two-hybrid screening and did not interact with either of the human IMPDH proteins. The present study highlightsthe potential of Phylomer peptides as target validation tools for Cryptosporidium and other organisms and diseases because of their ability to bind with high affinity to target proteins and disrupt function.
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Affiliation(s)
- R Jefferies
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia; Phylogica, Telethon Institute for Child Health Research, Subiaco, Western Australia, Australia
| | - R Yang
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia
| | - C K Woh
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia; Phylogica, Telethon Institute for Child Health Research, Subiaco, Western Australia, Australia
| | - T Weldt
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia
| | - N Milech
- Phylogica, Telethon Institute for Child Health Research, Subiaco, Western Australia, Australia
| | - A Estcourt
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia
| | - T Armstrong
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia
| | - R Hopkins
- Phylogica, Telethon Institute for Child Health Research, Subiaco, Western Australia, Australia
| | - P Watt
- Phylogica, Telethon Institute for Child Health Research, Subiaco, Western Australia, Australia
| | - S Reid
- School of Population Health, The University of Queensland, Herston, Queensland, Australia
| | - A Armson
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia
| | - U M Ryan
- School of Veterinary and Life Sciences, Murdoch University, Western Australia, Australia.
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24
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Singh G, Ghosh U, Pal S, Ampapathi RS, Chakraborty TK. βγ-fused turn structures in sugar amino acid (SAA) containing cyclic tetrapeptides with α3δ architecture. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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25
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Gao B, Zhu S. An insect defensin-derived β-hairpin peptide with enhanced antibacterial activity. ACS Chem Biol 2014; 9:405-13. [PMID: 24228718 DOI: 10.1021/cb400591d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Insect defensins are a class of small, cysteine-rich antimicrobial peptides primarily active on Gram-positive bacteria. Their roles in maggot therapy for treating chronic wound infection have been reported recently. However, a relatively narrow antibacterial spectrum together with the lack of a cost-effective means of commercial-scale production has limited their application. To further exploit the therapeutic potential of these molecules, we engineered the carboxyl-terminal β-sheet of navidefensin2-2, an insect defensin from Nasonia vitripennis, based on its structural similarity to naturally occurring microbicidal β-hairpin peptides. The designed peptide of 14 residues, referred to as NvBH, spans the β-sheet region of the defensin with two amino acids substituted for assembly of a disulfide-bonded amphipathic β-hairpin structure. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) combined with circular dichroism (CD) analysis shows that the oxidized NvBH (oNvBH), produced from the synthetic peptide by air oxidization in an alkaline environment, folds into a typical β-hairpin structure linked by two disulfide bridges (Cys1-Cys4; Cys2-Cys3). However, such a structure appears not to be functionally necessary as synthetic NvBH with a spontaneously oxidized disulfide bridge (Cys2-Cys3) (termed poNvBH) displayed similar antibacterial potency to oNvBH. In comparison with oNvBH, poNvBH exhibited higher serum stability and more resistance on tryptic digestion. These two forms of peptides are capable of killing an array of Gram-positive (including antibiotic-resistant strains of Staphylococcus) and Gram-negative bacterial pathogens at low micromolar concentrations through a membrane disruptive mode of action. Our work indicates that the β-sheet region of insect defensins is a promising subdomain of proteins in anti-infective drug discovery.
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Affiliation(s)
- Bin Gao
- Group of
Animal Innate Immunity, State Key Laboratory of Integrated Management
of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Shunyi Zhu
- Group of
Animal Innate Immunity, State Key Laboratory of Integrated Management
of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
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26
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Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes. Proc Natl Acad Sci U S A 2014; 111:2542-7. [PMID: 24550280 DOI: 10.1073/pnas.1312296111] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human proteome contains a plethora of short linear motifs (SLiMs) that serve as binding interfaces for modular protein domains. Such interactions are crucial for signaling and other cellular processes, but are difficult to detect because of their low to moderate affinities. Here we developed a dedicated approach, proteomic peptide-phage display (ProP-PD), to identify domain-SLiM interactions. Specifically, we generated phage libraries containing all human and viral C-terminal peptides using custom oligonucleotide microarrays. With these libraries we screened the nine PSD-95/Dlg/ZO-1 (PDZ) domains of human Densin-180, Erbin, Scribble, and Disks large homolog 1 for peptide ligands. We identified several known and putative interactions potentially relevant to cellular signaling pathways and confirmed interactions between full-length Scribble and the target proteins β-PIX, plakophilin-4, and guanylate cyclase soluble subunit α-2 using colocalization and coimmunoprecipitation experiments. The affinities of recombinant Scribble PDZ domains and the synthetic peptides representing the C termini of these proteins were in the 1- to 40-μM range. Furthermore, we identified several well-established host-virus protein-protein interactions, and confirmed that PDZ domains of Scribble interact with the C terminus of Tax-1 of human T-cell leukemia virus with micromolar affinity. Previously unknown putative viral protein ligands for the PDZ domains of Scribble and Erbin were also identified. Thus, we demonstrate that our ProP-PD libraries are useful tools for probing PDZ domain interactions. The method can be extended to interrogate all potential eukaryotic, bacterial, and viral SLiMs and we suggest it will be a highly valuable approach for studying cellular and pathogen-host protein-protein interactions.
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27
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Saito K, Nakato M, Mizuguchi T, Wada S, Uchimura H, Kataoka H, Yokoyama S, Hirota H, Kiso Y. Application of plug-plug technique to ACE experiments for discovery of peptides binding to a larger target protein: A model study of calmodulin-binding fragments selected from a digested mixture of reduced BSA. Electrophoresis 2014; 35:846-54. [DOI: 10.1002/elps.201300339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/28/2013] [Accepted: 10/31/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Kazuki Saito
- Laboratory of Proteomic Sciences; 21st Century COE Program; Kyoto Pharmaceutical University; Kyoto Japan
- Department of Integrated Biosciences; Graduate School of Frontier Sciences; University of Tokyo; Kashiwa Chiba Japan
- Laboratory of Next Generation Drug Development; Graduate School of Frontier Sciences; University of Tokyo; Kashiwa Chiba Japan
- Protein Research Group; RIKEN Genomic Sciences Center; Tsurumi Yokohama Japan
| | - Mamiko Nakato
- Department of Medicinal Chemistry; Center for Frontier Research in Medicinal Science; Kyoto Pharmaceutical University; Yamashina-ku Kyoto Japan
| | - Takaaki Mizuguchi
- Department of Medicinal Chemistry; Center for Frontier Research in Medicinal Science; Kyoto Pharmaceutical University; Yamashina-ku Kyoto Japan
| | - Shinji Wada
- Department of Medicinal Chemistry; Center for Frontier Research in Medicinal Science; Kyoto Pharmaceutical University; Yamashina-ku Kyoto Japan
| | - Hiromasa Uchimura
- Laboratory of Proteomic Sciences; 21st Century COE Program; Kyoto Pharmaceutical University; Kyoto Japan
| | - Hiroshi Kataoka
- Department of Integrated Biosciences; Graduate School of Frontier Sciences; University of Tokyo; Kashiwa Chiba Japan
| | - Shigeyuki Yokoyama
- Protein Research Group; RIKEN Genomic Sciences Center; Tsurumi Yokohama Japan
| | - Hiroshi Hirota
- Protein Research Group; RIKEN Genomic Sciences Center; Tsurumi Yokohama Japan
| | - Yoshiaki Kiso
- Department of Medicinal Chemistry; Center for Frontier Research in Medicinal Science; Kyoto Pharmaceutical University; Yamashina-ku Kyoto Japan
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Li F, Fan J, Wu Z, Liu RY, Guo L, Dong Z, Wang Z. Reversal effects of Rabdosia rubescens extract on multidrug resistance of MCF-7/Adr cells in vitro. PHARMACEUTICAL BIOLOGY 2013; 51:1196-1203. [PMID: 23777360 DOI: 10.3109/13880209.2013.784342] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
CONTEXT Rabdosia rubescens (Hemsl.) Hara (Lamiaceae) is widely used in traditional Chinese medicines for the treatment of antitumor, antimicrobial, anti-inflammatory and antioxidation. It is also used as a supplement in the treatment of many cancers, such as esophagus, mammary gland, liver and prostate cancers. OBJECTIVE To investigate the multidrug resistance (MDR) reversal effects and its possible mechanism of R. rubescens extracts on human breast cancer cell line MCF-7/Adr (Michigan Cancer Foundation--7/adriamycin resistance). MATERIALS AND METHODS Rabdosia rubescens were extracted by reflux extraction method with different solvent such as petroleum ether, chloroform, ethyl acetate, n-butyl alcohol and water in order and obtain petroleum ether fraction (PEF), chloroform fraction (CF), ethyl acetate fraction (EAF), n-butyl alcohol fraction (BAF) and aqueous fraction (AF). The active extract fractions of R. rubescens were screened by rhodamine123 (Rh123) accumulation assay. Cytotoxicity of the effect fraction was examined by the MTT assay; the intracellular accumulation of adriamycin and expression of P-gp were examined by flow cytometry; the gene transcription of MDR1 was determined by RT-PCR. RESULTS CF and EAF fractions could increase the intracellular accumulation of adriamycin in MCF-7/Adr cells, PEF, BAF and AF fractions showed little effect on the intracellular accumulation of adriamycin or Rh123. When adriamycin was used in combination with CF and EAF fractions at non-toxic concentration on MCF-7/Adr cells, CF and EAF fractions can reverse MDR of MCF-7/Adr cells, and the reverse folds were 2.16 (CF, 4 μg/mL), 4.60 (CF, 20 μg/mL), 1.87 (EAF, 4 μg/mL) and 4.02 (EAF, 20 μg/mL), respectively. After treatment with CF (4.20 μg/mL) and EAF (4.20 μg/mL) for 48 h, the MDR1 gene expression level in MCF-7/Adr cells was decreased by 40.17, 48.14, 33.86 and 42.52%, and the abundance of P-gp also decreased by 8.63, 24.53, 27.50 and 34.91% in MCF-7/Adr cells, respectively. DISCUSSION AND CONCLUSION These results indicate the therapeutic value of chloroform fraction (CF) and ethyl acetate fraction (EAF) from R. rubescens as potential MDR reversing agents and warranted further investigation.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B
- ATP Binding Cassette Transporter, Subfamily B, Member 1/antagonists & inhibitors
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- Antibiotics, Antineoplastic/metabolism
- Antibiotics, Antineoplastic/therapeutic use
- Antineoplastic Agents, Phytogenic/isolation & purification
- Antineoplastic Agents, Phytogenic/pharmacology
- Biological Transport/drug effects
- Breast Neoplasms/drug therapy
- Breast Neoplasms/metabolism
- Caco-2 Cells
- Doxorubicin/metabolism
- Doxorubicin/therapeutic use
- Drug Resistance, Multiple/drug effects
- Drug Resistance, Neoplasm/drug effects
- Drugs, Chinese Herbal/isolation & purification
- Drugs, Chinese Herbal/pharmacology
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Isodon/chemistry
- MCF-7 Cells
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Plant Components, Aerial/chemistry
- Plant Extracts/isolation & purification
- Plant Extracts/pharmacology
- Solvents/chemistry
- Up-Regulation/drug effects
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Affiliation(s)
- Farong Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
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29
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A novel retro-inverso peptide is a preferential JNK substrate-competitive inhibitor. Int J Biochem Cell Biol 2013; 45:1939-50. [DOI: 10.1016/j.biocel.2013.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/04/2013] [Accepted: 06/11/2013] [Indexed: 12/22/2022]
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30
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Duran-Frigola M, Mosca R, Aloy P. Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development. ACTA ACUST UNITED AC 2013; 20:674-84. [DOI: 10.1016/j.chembiol.2013.03.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/28/2013] [Accepted: 03/05/2013] [Indexed: 01/12/2023]
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31
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Wise MJ. Mean protein evolutionary distance: a method for comparative protein evolution and its application. PLoS One 2013; 8:e61276. [PMID: 23613826 PMCID: PMC3626687 DOI: 10.1371/journal.pone.0061276] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 03/08/2013] [Indexed: 12/26/2022] Open
Abstract
Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins’ roles. Different species’ proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.
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Affiliation(s)
- Michael J Wise
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia.
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Verschueren E, Vanhee P, Rousseau F, Schymkowitz J, Serrano L. Protein-peptide complex prediction through fragment interaction patterns. Structure 2013; 21:789-97. [PMID: 23583037 DOI: 10.1016/j.str.2013.02.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 01/13/2023]
Abstract
The number of protein-peptide interactions in a cell is so large that experimental determination of all these complex structures would be a daunting task. Although homology modeling and refinement protocols have vastly improved the number and quality of predicted structural models, ab initio methods are still challenged by both the large number of possible docking sites and the conformational space accessible to flexible peptides. We present a method that addresses these challenges by sampling the entire accessible surface of a protein with a reduced conformational space of interacting backbone fragment pairs from unrelated structures. We demonstrate its potential by predicting ab initio the bound structure for a variety of protein-peptide complexes. In addition, we show the potential of our method for the discovery of domain interaction sites and domain-domain docking.
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Affiliation(s)
- Erik Verschueren
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation-CRG, Dr. Aiguader 88, 08003 Barcelona, Spain
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Li FR, Fu YY, Jiang DH, Wu Z, Zhou YJ, Guo L, Dong ZM, Wang ZZ. Reversal effect of rosmarinic acid on multidrug resistance in SGC7901/Adr cell. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2013; 15:276-85. [PMID: 23421517 DOI: 10.1080/10286020.2012.762910] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Multidrug resistance (MDR) has been a major problem in cancer chemotherapy. In this study, the aim was to explore the reversal effect and its potential mechanism of rosmarinic acid (RA) on SGC7901/Adr cells. 3-(4,5-Dimethylthiazol)-2,5-diphenyl tetrazolium bromide (MTT) assay was used to investigate the reversal index of RA in SGC7901/Adr cell line. The intracellular accumulation of adriamycin, rhodamine123 (Rh123), and the expression of P-glycoprotein (P-gp) were assayed by flow cytometry. The influence of RA on the transcription of MDR1 gene was determined by reverse transcription-polymerase chain reaction. The results showed that RA could reverse the MDR of SGC7901/Adr cells, increase the intracellular accumulation of Adr and Rh123, and decrease the transcription of MDR1 gene and the expression of P-gp in SGC7901/Adr cells. These results indicated that RA was a potential multidrug resistance-reversing agent and warranted further investigations.
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Affiliation(s)
- Fa-Rong Li
- Key Laboratory of Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
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34
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Halder SK, Matsunaga H, Yamaguchi H, Ueda H. Novel neuroprotective action of prothymosin alpha-derived peptide against retinal and brain ischemic damages. J Neurochem 2013; 125:713-23. [DOI: 10.1111/jnc.12132] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 12/21/2022]
Affiliation(s)
- Sebok Kumar Halder
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - Hayato Matsunaga
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - Haruka Yamaguchi
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - Hiroshi Ueda
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
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Cruz-Migoni A, Fuentes-Fernandez N, Rabbitts TH. Peptides: minimal drug surrogates to interrogate and interfere with protein function. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00142c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The interactome in normal and disease cells is a key area for study and therapeutic targeting, yet few molecules have been developed that can interfere with protein–protein interactions within cells. Peptides and homologues are potential reagents to target PPI.
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Affiliation(s)
- A. Cruz-Migoni
- Weatherall Institute of Molecular Medicine
- MRC Molecular Haematology Unit
- University of Oxford
- John Radcliffe Hospital
- Oxford
| | - N. Fuentes-Fernandez
- Institute of Biological, Environmental and Rural Science
- Aberystwyth University
- Aberystwyth
- UK
| | - T. H. Rabbitts
- Weatherall Institute of Molecular Medicine
- MRC Molecular Haematology Unit
- University of Oxford
- John Radcliffe Hospital
- Oxford
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36
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Sun N, Funke SA, Willbold D. A survey of peptides with effective therapeutic potential in Alzheimer's disease rodent models or in human clinical studies. Mini Rev Med Chem 2012; 12:388-98. [PMID: 22303971 PMCID: PMC3426789 DOI: 10.2174/138955712800493942] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 06/21/2011] [Accepted: 07/07/2011] [Indexed: 11/29/2022]
Abstract
Alzheimer’s disease (AD) is a devastating neurodegenerative disorder and the most common cause of dementia. Today, only palliative therapies are available. The pathological hallmarks of AD are the presence of neurofibrillary tangles and amyloid plaques, mainly composed of the amyloid-β peptide (Aβ), in the brains of the patients. Several lines of evidence suggest that the increased production and/or decreased cleavage of Aβ and subsequent accumulation of Aβ oligomers and aggregates play a fundamental role in the disease progress. Therefore, substances which bind to Aβ and influence aggregation thereof are of great interest. A wide range of Aβ binding peptides were investigated to date for therapeutic purposes. Only very few were shown to be effective in rodent AD models or in clinical studies. Here, we review those peptides and discuss their possible mechanisms of action.
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Affiliation(s)
- N Sun
- ICS-6, Forschungszentrum Jülich, 52425 Jülich, Germany
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37
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Abstract
The current status of peptides that target the mitochondria in the context of cancer is the focus of this review. Chemotherapy and radiotherapy used to kill tumor cells are principally mediated by the process of apoptosis that is governed by the mitochondria. The failure of anticancer therapy often resides at the level of the mitochondria. Therefore, the mitochondrion is a key pharmacological target in cancer due to many of the differences that arise between malignant and healthy cells at the level of this ubiquitous organelle. Additionally, targeting the characteristics of malignant mitochondira often rely on disruption of protein--protein interactions that are not generally amenable to small molecules. We discuss anticancer peptides that intersect with pathological changes in the mitochondrion.
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38
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Russo LC, Asega AF, Castro LM, Negraes PD, Cruz L, Gozzo FC, Ulrich H, Camargo ACM, Rioli V, Ferro ES. Natural intracellular peptides can modulate the interactions of mouse brain proteins and thimet oligopeptidase with 14-3-3ε and calmodulin. Proteomics 2012; 12:2641-55. [DOI: 10.1002/pmic.201200032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 05/31/2012] [Accepted: 06/03/2012] [Indexed: 02/03/2023]
Affiliation(s)
- Lilian C. Russo
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Amanda F. Asega
- Laboratory of Applied Toxinology (LETA); Butantan Institute; SP Brazil
| | - Leandro M. Castro
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Priscilla D. Negraes
- Biochemistry Department; Chemistry Institute; University of São Paulo; São Paulo Brazil
| | - Lilian Cruz
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
| | - Fabio C. Gozzo
- Chemistry Institute; Campinas State University; Campinas SP Brazil
| | - Henning Ulrich
- Biochemistry Department; Chemistry Institute; University of São Paulo; São Paulo Brazil
| | | | - Vanessa Rioli
- Laboratory of Applied Toxinology (LETA); Butantan Institute; SP Brazil
| | - Emer S. Ferro
- Department of Cell Biology and Development; Biomedical Sciences Institute; University of São Paulo; São Paulo Brazil
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Milašinović N, Knežević-Jugović Z, Milosavljević N, Filipović J, Kalagasidis Krušić M. Controlled release of lipase from Candida rugosa loaded into hydrogels of N-isopropylacrylamide and itaconic acid. Int J Pharm 2012; 436:332-40. [PMID: 22759642 DOI: 10.1016/j.ijpharm.2012.06.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/31/2012] [Accepted: 06/24/2012] [Indexed: 10/28/2022]
Abstract
The series of poly(N-isopropylacrylamide-co-itaconic acid) hydrogels, with lipase from Candida rugosa as a model protein, were synthesized by free radical copolymerization. The composition of hydrogels was varied by monomers ratio, crosslinking agent concentration and amounts of lipase, which was loaded by in situ polymerization. All samples were characterized regarding morphology. The investigation of hydrogel swelling properties revealed their pH and temperature sensitive character. Protein loading efficiency, release profiles and the specific activity yield of the released lipase were also investigated as a function of hydrogel composition, protein content and pH, at the physiological temperature of 37 °C. Copolymers of N-isopropylacrylamide and itaconic acid presented high lipase loading efficiency. Another very important feature of these copolymers was that the protein release kinetic strongly depended on the pH value of the medium. The diffusion exponents values around 1 denoted that these hydrogel compositions could be adjusted to follow near zero-order kinetics. Namely, hydrogel formulations released low amounts of lipase at pH 2.20, but much higher released protein quantities were observed at pH 6.80 enabling these copolymers to be attractive candidates as site specific protein oral drug delivery systems.
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Affiliation(s)
- Nikola Milašinović
- University of Belgrade, Faculty of Technology and Metallurgy, Department of Organic Chemical Technology, Karnegijeva 4, 11000 Belgrade, Serbia.
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40
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Development of anti-infectives using phage display: biological agents against bacteria, viruses, and parasites. Antimicrob Agents Chemother 2012; 56:4569-82. [PMID: 22664969 DOI: 10.1128/aac.00567-12] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The vast majority of anti-infective therapeutics on the market or in development are small molecules; however, there is now a nascent pipeline of biological agents in development. Until recently, phage display technologies were used mainly to produce monoclonal antibodies (MAbs) targeted against cancer or inflammatory disease targets. Patent disputes impeded broad use of these methods and contributed to the dearth of candidates in the clinic during the 1990s. Today, however, phage display is recognized as a powerful tool for selecting novel peptides and antibodies that can bind to a wide range of antigens, ranging from whole cells to proteins and lipid targets. In this review, we highlight research that exploits phage display technology as a means of discovering novel therapeutics against infectious diseases, with a focus on antimicrobial peptides and antibodies in clinical or preclinical development. We discuss the different strategies and methods used to derive, select, and develop anti-infectives from phage display libraries and then highlight case studies of drug candidates in the process of development and commercialization. Advances in screening, manufacturing, and humanization technologies now mean that phage display can make a significant contribution in the fight against clinically important pathogens.
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41
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Milletti F. Cell-penetrating peptides: classes, origin, and current landscape. Drug Discov Today 2012; 17:850-60. [PMID: 22465171 DOI: 10.1016/j.drudis.2012.03.002] [Citation(s) in RCA: 586] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 01/04/2012] [Accepted: 03/07/2012] [Indexed: 11/24/2022]
Abstract
With more than ten new FDA approvals since 2001, peptides are emerging as an important therapeutic alternative to small molecules. However, unlike small molecules, peptides on the market today are limited to extracellular targets. By contrast, cell-penetrating peptides (CPPs) can target intracellular proteins and also carry other cargoes (e.g. other peptides, small molecules or proteins) into the cell, thus offering great potential as future therapeutics. In this review I present a classification scheme for CPPs based on their physical-chemical properties and origin, and I provide a general framework for understanding and discovering new CPPs.
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Affiliation(s)
- Francesca Milletti
- Hoffmann-La Roche Inc., pRED Informatics, 340 Kingsland Street, Nutley, NJ, USA.
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42
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Kim S, Kim D, Jung HH, Lee IH, Kim JIL, Suh JY, Jon S. Bio-Inspired Design and Potential Biomedical Applications of a Novel Class of High-Affinity Peptides. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107894] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Kim S, Kim D, Jung HH, Lee IH, Kim JIL, Suh JY, Jon S. Bio-Inspired Design and Potential Biomedical Applications of a Novel Class of High-Affinity Peptides. Angew Chem Int Ed Engl 2012; 51:1890-4. [DOI: 10.1002/anie.201107894] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 12/12/2011] [Indexed: 12/18/2022]
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Milech N, Watt P. The construction of "phylomer" peptide libraries as a rich source of potent inhibitors of protein/protein interactions. Methods Mol Biol 2012; 899:43-60. [PMID: 22735945 DOI: 10.1007/978-1-61779-921-1_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Phylomer libraries are made from random overlapping genome fragments of biodiverse bacteria and Archaea. They provide a rich source of high-affinity binders to protein interfaces, and can be used both for target-directed screening approaches and for phenotypic screens to discover new targets. Here, we describe methods used for the construction of a Phylomer library, illustrated by examples of construction in both a yeast two-hybrid vector and a phage display vector.
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Affiliation(s)
- Nadia Milech
- Telethon Institute for Child Heath Research and Centre for Child Health, University of Western Australia, Subiaco, WA, Australia.
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45
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Katsila T, Siskos AP, Tamvakopoulos C. Peptide and protein drugs: the study of their metabolism and catabolism by mass spectrometry. MASS SPECTROMETRY REVIEWS 2012; 31:110-133. [PMID: 21698655 DOI: 10.1002/mas.20340] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Peptide and protein drugs have evolved in recent years into mainstream therapeutics, representing a significant portion of the pharmaceutical market. Peptides and proteins exhibit highly diverse structures, broad biological activities as hormones, neurotransmitters, structural proteins, metabolic modulators and therefore have a significant role as both therapeutics and biomarkers. Understanding the metabolism of synthetic or biotechnologically derived peptide and protein drugs is critical for pharmaceutical development as metabolism has a significant impact on drug efficacy and safety. Although the same principles of pharmacokinetics and metabolism of small molecule drugs apply to peptide and protein drugs, there are few notable differences. Moreover, the study of peptide and protein drug metabolism is a rather complicated process which requires sophisticated analytical techniques, and mass spectrometry based approaches have provided the capabilities for efficient and reliable quantification, characterization, and metabolite identification. This review article will focus on the current use of mass spectrometry for the study of the metabolism of peptide and protein drugs.
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Affiliation(s)
- Theodora Katsila
- Biomedical Research Foundation, Academy of Athens, Division of Pharmacology-Pharmacotechnology, Soranou Efesiou Street 4, Athens GR-11527, Greece
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46
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Ullman CG, Frigotto L, Cooley RN. In vitro methods for peptide display and their applications. Brief Funct Genomics 2011; 10:125-34. [PMID: 21628313 DOI: 10.1093/bfgp/elr010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The presentation of recombinant peptide libraries linked to their coding sequence can be referred to as 'peptide display'. Phage display is the most widely practiced peptide display technology but more recent alternatives such as CIS display, ribosome display and mRNA display offer advantages over phage for speed, library size and the display of unnatural amino acids. These have provided researchers with tools to address some of the failings of peptides such as their low affinity, low stability and inability to cross biological membranes. In this review, we assess some of the recent advances in peptide display and its application.
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Affiliation(s)
- Christopher G Ullman
- Isogenica Ltd., The Mansion, Chesterford Research Park, Little Chesterford, Essex, UK.
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47
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Phenotypic screening of phylomer peptide libraries derived from genome fragments to identify and validate new targets and therapeutics. Future Med Chem 2011; 1:257-65. [PMID: 21425969 DOI: 10.4155/fmc.09.28] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Phenotypic screening of random peptide libraries has been hampered by very poor hit rates. This is probably due to the fact that random combinatorial peptide libraries contain an insufficiently large proportion of secondary and/or tertiary structures that are likely to interact in a stable manner with multiple classes of potential target proteins. Phylomer libraries, by contrast, are derived from sequences of genomes that have been through millions to billions of years of evolution and were therefore hypothesized to be more likely to encode appropriate structures, which have been selected to stably bind with high affinity to protein surfaces. This approach is analogous to small-molecule libraries constructed to provide a rich source of structures (often found in natural products) that are common to the pharmacophores of known drugs. DISCUSSION Phenotypic screens of phylomer libraries show very high hit rates for bioactive peptides, suggesting that they may be a useful tool for target discovery and validation. Biophysical evidence suggests that this high activity may be due to the high proportion of affinities of unmodified peptides in the low nanomolar range. CONCLUSION The high hit rates from phylomer libraries are sufficient to allow libraries composed of synthetic peptides to be synthesized and screened in parallel high-throughput screening formats. In addition to allowing the identification of new targets, the phylomer peptides themselves may be useful as structural probes to map epitopes of target vulnerability and as leads in therapeutic discovery.
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48
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Zhang H, Curreli F, Zhang X, Bhattacharya S, Waheed AA, Cooper A, Cowburn D, Freed EO, Debnath AK. Antiviral activity of α-helical stapled peptides designed from the HIV-1 capsid dimerization domain. Retrovirology 2011; 8:28. [PMID: 21539734 PMCID: PMC3097154 DOI: 10.1186/1742-4690-8-28] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 05/03/2011] [Indexed: 01/11/2023] Open
Abstract
Background The C-terminal domain (CTD) of HIV-1 capsid (CA), like full-length CA, forms dimers in solution and CTD dimerization is a major driving force in Gag assembly and maturation. Mutations of the residues at the CTD dimer interface impair virus assembly and render the virus non-infectious. Therefore, the CTD represents a potential target for designing anti-HIV-1 drugs. Results Due to the pivotal role of the dimer interface, we reasoned that peptides from the α-helical region of the dimer interface might be effective as decoys to prevent CTD dimer formation. However, these small peptides do not have any structure in solution and they do not penetrate cells. Therefore, we used the hydrocarbon stapling technique to stabilize the α-helical structure and confirmed by confocal microscopy that this modification also made these peptides cell-penetrating. We also confirmed by using isothermal titration calorimetry (ITC), sedimentation equilibrium and NMR that these peptides indeed disrupt dimer formation. In in vitro assembly assays, the peptides inhibited mature-like virus particle formation and specifically inhibited HIV-1 production in cell-based assays. These peptides also showed potent antiviral activity against a large panel of laboratory-adapted and primary isolates, including viral strains resistant to inhibitors of reverse transcriptase and protease. Conclusions These preliminary data serve as the foundation for designing small, stable, α-helical peptides and small-molecule inhibitors targeted against the CTD dimer interface. The observation that relatively weak CA binders, such as NYAD-201 and NYAD-202, showed specificity and are able to disrupt the CTD dimer is encouraging for further exploration of a much broader class of antiviral compounds targeting CA. We cannot exclude the possibility that the CA-based peptides described here could elicit additional effects on virus replication not directly linked to their ability to bind CA-CTD.
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Affiliation(s)
- Hongtao Zhang
- Laboratory of Molecular Modeling & Drug Design; Lindsley F, Kimball Research Institute of the New York Blood Center, 310 E 67th Street, New York, NY 10065, USA
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49
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Hernández‐Toribio J, Gómez Arrayás R, Carretero JC. Enantiocontrolled Synthesis of β‐Branched α‐Amino Acids by Using Cu
I
‐Catalyzed 1,4‐Addition of Glycine Imines to β‐Substituted
gem
‐Diactivated Olefins. Chemistry 2011; 17:6334-7. [DOI: 10.1002/chem.201100374] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Jorge Hernández‐Toribio
- Departamento de Química Orgánica, Universidad Autónoma de Madrid (UAM), Facultad de Ciencias, Cantoblanco, 28049 Madrid (Spain), Fax: (+34) 91‐497‐3966
| | - Ramón Gómez Arrayás
- Departamento de Química Orgánica, Universidad Autónoma de Madrid (UAM), Facultad de Ciencias, Cantoblanco, 28049 Madrid (Spain), Fax: (+34) 91‐497‐3966
| | - Juan C. Carretero
- Departamento de Química Orgánica, Universidad Autónoma de Madrid (UAM), Facultad de Ciencias, Cantoblanco, 28049 Madrid (Spain), Fax: (+34) 91‐497‐3966
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50
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Johannessen L, Remsberg J, Gaponenko V, Adams KM, Barchi JJ, Tarasov SG, Jiang S, Tarasova NI. Peptide structure stabilization by membrane anchoring and its general applicability to the development of potent cell-permeable inhibitors. Chembiochem 2011; 12:914-21. [PMID: 21365731 DOI: 10.1002/cbic.201000563] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Indexed: 11/08/2022]
Abstract
Isolated protein motifs that are involved in interactions with their binding partners can be used to inhibit these interactions. However, peptides corresponding to protein fragments tend to have no defined secondary or tertiary structure in the absence of scaffolding by the rest of protein molecule. This results in low inhibitor potency. NMR and CD spectroscopy studies of lipopeptide inhibitors of the Hedgehog pathway revealed that membrane anchoring allows the cell membrane to function as a scaffold and facilitate the folding of short peptides. In addition, lipidation enhances cell permeability and increases the concentration of the compounds near the membrane, thus facilitating potent inhibition. The general applicability of this rational approach was further confirmed by the generation of selective antagonists of the insulin-like growth factor 1 receptor with GI(50) values in the nanomolar range. Lipopeptides corresponding to protein fragments were found to serve as potent and selective inhibitors of a number of nondruggable molecular targets.
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Affiliation(s)
- Liv Johannessen
- Cancer and Inflammation Program, Center for Cancer Research NCI-Frederick, Frederick, MD, 21702, USA
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