1
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Surface chemistry dependent toxicity of inorganic nanostructure glycoconjugates on bacterial cells and cancer cell lines. J Drug Deliv Sci Technol 2023. [DOI: 10.1016/j.jddst.2022.104054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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2
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Azari-Anpar M, Degraeve P, Oulahal N, Adt I, Jahanbin K, Demarigny Y, Assifaoui A, Tabatabaei Yazdi F. Interaction of Escherichia coli heat-labile enterotoxin B-pentamer with exopolysaccharides from Leuconostoc mesenteroides P35: Insights from surface plasmon resonance and molecular docking studies. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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3
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Badshah SL, Naeem A. Computational Simulation of Conjugated Cholera Toxin Protein. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2021. [DOI: 10.3103/s0891416821050049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Lin M, Zhang J, Wan H, Yan C, Xia F. Rationally Designed Multivalent Aptamers Targeting Cell Surface for Biomedical Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9369-9389. [PMID: 33146988 DOI: 10.1021/acsami.0c15644] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Specific interactions between ligands and receptors on cell surface play an important role in the cell biological process. Nucleic acid aptamers as commonly used ligands enable specific recognition and tight binding to membrane protein receptors for modulation of cell fate. Therefore, molecular probes with aptamers can be applied for cancer diagnosis and targeted therapy by targeting overexpression membrane proteins of cancer cells. However, because of their fast degradation and rapid glomerulus clearance in vivo, the applications of aptamers in physiological conditions remain challenged. Inspired by natural multivalent interactions, many approaches have been developed to construct multivalent aptamers to improve the performance of aptamers in complex matrices with higher binding affinity, more stability, and longer circulation time. In this review, we first introduce the aptamer generation from purified protein-based SELEX and whole cell-based SELEX for targeting the cell surface. We then highlight the approaches to fabricate multivalent aptamers and discuss their properties. By integrating different materials (including inorganic nanomaterials, diacyllipid, polymeric nanoparticles, and DNA nanostructures) as scaffolds with an interface modification technique, we have summarized four kinds of multivalent aptamers. After that, representative applications in biosensing and targeted therapy are illustrated to show the elevated performance of multivalent aptamers. In addition, we analyze the challenges and opportunities for the clinical practices of multivalent aptamers.
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Affiliation(s)
- Meihua Lin
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jian Zhang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Hao Wan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Chengyang Yan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
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5
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Bisindolylmaleimide IX: A novel anti-SARS-CoV2 agent targeting viral main protease 3CLpro demonstrated by virtual screening pipeline and in-vitro validation assays. Methods 2021; 195:57-71. [PMID: 33453392 PMCID: PMC7807167 DOI: 10.1016/j.ymeth.2021.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/10/2021] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2, the virus that causes COVID-19 consists of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs/compounds. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2'-O-MT. For virtual screening, energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard (Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs and investigational molecules (n = 5903). The screening was performed against viral targets using three sequential docking modes (i.e., HTVS, SP, and XP). Virtual screening identified ∼290 potential inhibitors based on the criteria of energy, docking parameters, ligand, and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. The top lead from each target pool was further subjected to molecular dynamics simulation using the Desmond module. The resulting top eight hits were tested for their SARS-CoV-2 anti-viral activity in-vitro. Among these, a known inhibitor of protein kinase C isoforms, Bisindolylmaleimide IX (BIM IX), was found to be a potent inhibitor of SARS-CoV-2. Further, target validation through enzymatic assays confirmed 3CLpro to be the target. This is the first study that has showcased BIM IX as a COVID-19 inhibitor thereby validating our pipeline.
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6
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Monaco S, Walpole S, Doukani H, Nepravishta R, Martínez‐Bailén M, Carmona AT, Ramos‐Soriano J, Bergström M, Robina I, Angulo J. Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B. Chemistry 2020; 26:10024-10034. [PMID: 32449563 PMCID: PMC7496166 DOI: 10.1002/chem.202001723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/08/2020] [Indexed: 11/30/2022]
Abstract
Ligand-based NMR techniques to study protein-ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi-frequency STD NMR approach, differential epitope mapping (DEEP)-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so-called DEEP-STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin.
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Affiliation(s)
- Serena Monaco
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Samuel Walpole
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Hassan Doukani
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Ridvan Nepravishta
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Biochemistry & Molecular BiologySealy Center for Structural Biology & Molecular BiophysicsUniversity of Texas Medical Branch301 University BlvdGalvestonTX77555-1068USA
| | | | - Ana T. Carmona
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Javier Ramos‐Soriano
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Maria Bergström
- Department of Chemistry and Biomedical SciencesLinnaeus University391 82KalmarSweden
| | - Inmaculada Robina
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Jesus Angulo
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
- Instituto de Investigaciones Químicas (CSIC-US)Avda. Américo Vespucio, 4941092SevillaSpain
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7
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Sousa FBM, Nolêto IRSG, Chaves LS, Pacheco G, Oliveira AP, Fonseca MMV, Medeiros JVR. A comprehensive review of therapeutic approaches available for the treatment of cholera. J Pharm Pharmacol 2020; 72:1715-1731. [DOI: 10.1111/jphp.13344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/04/2020] [Indexed: 12/15/2022]
Abstract
Abstract
Objectives
The oral rehydration solution is the most efficient method to treat cholera; however, it does not interfere in the action mechanism of the main virulence factor produced by Vibrio cholerae, the cholera toxin (CT), and this disease still stands out as a problem for human health worldwide. This review aimed to describe therapeutic alternatives available in the literature, especially those related to the search for molecules acting upon the physiopathology of cholera.
Key findings
New molecules have offered a protection effect against diarrhoea induced by CT or even by infection from V. cholerae. The receptor regulator cystic fibrosis channel transmembrane (CFTR), monosialoganglioside (GM1), enkephalinase, AMP-activated protein kinase (AMPK), inhibitors of expression of virulence factors and activators of ADP-ribosylarginine hydrolase are the main therapeutic targets studied. Many of these molecules or extracts still present unclear action mechanisms.
Conclusions
Knowing therapeutic alternatives and their molecular mechanisms for the treatment of cholera could guide us to develop a new drug that could be used in combination with the rehydration solution.
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Affiliation(s)
- Francisca B M Sousa
- Laboratory of Pharmacology of Inflammation and Gastrointestinal Disorders (Lafidg), Post-graduation Program in Biotechnology, Federal University of Parnaíba Delta, Parnaíba, Brazil
- Northeast Biotechnology Network (RENORBIO), Federal University of Piauí, Teresina, Brazil
| | - Isabela R S G Nolêto
- Laboratory of Pharmacology of Inflammation and Gastrointestinal Disorders (Lafidg), Post-graduation Program in Biotechnology, Federal University of Parnaíba Delta, Parnaíba, Brazil
- Northeast Biotechnology Network (RENORBIO), Federal University of Piauí, Teresina, Brazil
| | - Leticia S Chaves
- Laboratory of Pharmacology of Inflammation and Gastrointestinal Disorders (Lafidg), Post-graduation Program in Biotechnology, Federal University of Parnaíba Delta, Parnaíba, Brazil
- Post-graduation Program in Biomedical Sciences, Federal University of Piauí, Parnaíba, Brazil
| | - Gabriella Pacheco
- Laboratory of Pharmacology of Inflammation and Gastrointestinal Disorders (Lafidg), Post-graduation Program in Biotechnology, Federal University of Parnaíba Delta, Parnaíba, Brazil
| | - Ana P Oliveira
- Laboratory of Pharmacology of Inflammation and Gastrointestinal Disorders (Lafidg), Post-graduation Program in Biotechnology, Federal University of Parnaíba Delta, Parnaíba, Brazil
- Northeast Biotechnology Network (RENORBIO), Federal University of Piauí, Teresina, Brazil
| | - Mikhail M V Fonseca
- Institute of Higher Education of Vale do Parnaíba (IESVAP), Parnaíba, Brazil
| | - Jand V R Medeiros
- Laboratory of Pharmacology of Inflammation and Gastrointestinal Disorders (Lafidg), Post-graduation Program in Biotechnology, Federal University of Parnaíba Delta, Parnaíba, Brazil
- Northeast Biotechnology Network (RENORBIO), Federal University of Piauí, Teresina, Brazil
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8
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Biopolymer Extracted from Anadenanthera colubrina (Red Angico Gum) Exerts Therapeutic Potential in Mice: Antidiarrheal Activity and Safety Assessment. Pharmaceuticals (Basel) 2020; 13:ph13010017. [PMID: 31963683 PMCID: PMC7168896 DOI: 10.3390/ph13010017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Anadenanthera colubrina var. cebil (Griseb.) Altschul (Fabaceae family), commonly known as the red angico tree, is a medicinal plant found throughout Brazil’s semi-arid area. In this study, a chemical analysis was performed to investigate the antidiarrheal activity and safety profile of red angico gum (RAG), a biopolymer extracted from the trunk exudate of A. colubrina. Upon FT-IR spectroscopy, RAG showed bands in the regions of 1608 cm−1, 1368 cm−1, and 1029 cm−1, which relate to the vibration of O–H water molecules, deformation vibration of C-O bands, and vibration of the polysaccharide C-O band, respectively, all of which are relevant to glycosidic bonds. The peak molar mass of RAG was 1.89 × 105 g/mol, with the zeta potential indicating electronegativity. RAG demonstrated high yield and solubility with a low degree of impurity. Pre-treatment with RAG reduced the total diarrheal stool and enteropooling. RAG also enhanced Na+/K+-ATPase activity and reduced gastrointestinal transit, and thereby inhibited intestinal smooth muscle contractions. Enzyme-Linked Immunosorbent Assay (ELISA) demonstrated that RAG can interact with GM1 receptors and can also reduce E. coli-induced diarrhea in vivo. Moreover, RAG did not induce any signs of toxicity in mice. These results suggest that RAG is a possible candidate for the treatment of diarrheal diseases.
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9
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Bauzá A, Frontera A, Mooibroek TJ. π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures. Chemistry 2019; 25:13436-13443. [PMID: 31453653 PMCID: PMC6856858 DOI: 10.1002/chem.201903404] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 01/03/2023]
Abstract
Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.
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Affiliation(s)
- Antonio Bauzá
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta. de Valldemossa km 7.507122Palma (Baleares)Spain
| | - Tiddo Jonathan Mooibroek
- van ‘t Hoff Institute for Molecular SciencesUniversiteit van AmsterdamScience Park 9041098XHAmsterdamThe Netherlands
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10
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Krueger E, Brown AC. Inhibition of bacterial toxin recognition of membrane components as an anti-virulence strategy. J Biol Eng 2019; 13:4. [PMID: 30820243 PMCID: PMC6380060 DOI: 10.1186/s13036-018-0138-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/27/2018] [Indexed: 12/21/2022] Open
Abstract
Over recent years, the development of new antibiotics has not kept pace with the rate at which bacteria develop resistance to these drugs. For this reason, many research groups have begun to design and study alternative therapeutics, including molecules to specifically inhibit the virulence of pathogenic bacteria. Because many of these pathogenic bacteria release protein toxins, which cause or exacerbate disease, inhibition of the activity of bacterial toxins is a promising anti-virulence strategy. In this review, we describe several approaches to inhibit the initial interactions of bacterial toxins with host cell membrane components. The mechanisms by which toxins interact with the host cell membrane components have been well-studied over the years, leading to the identification of therapeutic targets, which have been exploited in the work described here. We review efforts to inhibit binding to protein receptors and essential membrane lipid components, complex assembly, and pore formation. Although none of these molecules have yet been demonstrated in clinical trials, the in vitro and in vivo results presented here demonstrate their promise as novel alternatives and/or complements to traditional antibiotics.
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Affiliation(s)
- Eric Krueger
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015 USA
| | - Angela C. Brown
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015 USA
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11
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Bezerra FF, Lima GC, Sousa NAD, Sousa WMD, Costa LEC, Costa DSD, Barros FCN, Medeiros JVR, Freitas ALP. Antidiarrheal activity of a novel sulfated polysaccharide from the red seaweed Gracilaria cervicornis. JOURNAL OF ETHNOPHARMACOLOGY 2018; 224:27-35. [PMID: 29803569 DOI: 10.1016/j.jep.2018.05.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The use of marine seaweeds as a source of natural compounds with medicinal purposes is increasing in Western countries in the last decades, becoming an important alternative in the traditional medicine of many developing countries, where diarrhea still remains a severe public health problem, with high rates of mortality and morbidity. Sulfated polysaccharides (PLS) extracted from red seaweeds can exhibit therapeutic effects for the treatment of gastrointestinal disorders. Thus, the pharmacological properties of the PLS from Gracilaria cervicornis, an endemic seaweed found in the Brazilian northeast coast, was evaluated as an alternative natural medication for diarrhea. AIM OF THE STUDY This study aimed to evaluate the antidiarrheal activity of sulfated polysaccharides (PLS) extracted from the red seaweed G. cervicornis in Swiss mice pre-treated with castor oil or cholera toxin. MATERIALS AND METHODS The seaweed Gracilaria cervicornis was collected at Flecheiras beach (city of Trairí, State of Ceará, Brazil) and the PLS was obtained through enzymatic extraction and administered in mice (25-30 g) before diarrhea induction with castor oil or cholera toxin. For the evaluation of the total number of fecal output and diarrheal feces, the animals were placed in cages lined with adsorbent material. The evaluation of intestinal fluid accumulation (enteropooling) on castor oil-induced diarrhea in mice occurred by dissecting the small intestine and measuring its volume. The determination of Na+/K+-ATPase activity was measured in the small intestine supernatants by colorimetry, using commercial biochemistry kits. The gastrointestinal motility was evaluated utilizing an activated charcoal as a food tracer. The intestinal fluid secretion and chloride ion concentration were evaluated in intestinal closed loops in mice with cholera toxin-induced secretory diarrhea. The binding ability of PLS with GM1 and/or cholera toxin was evaluated by an Enzyme-Linked Immunosorbent Assay (ELISA). RESULTS The G. cervicornis PLS showed antidiarrheal effects in both acute and secretory diarrhea, reducing the total number of fecal output, diarrheic stools, intestinal fluid accumulation, and increasing small intestine Na+/K+-ATPase activity on castor oil-induced diarrhea. However, the PLS did not affect gastrointestinal motility, indicating that this compound has a different action mechanism than loperamide. In secretory diarrhea, the PLS decreased intestinal fluid secretion and small intestine chloride excretion, binding with GM1 and/or cholera toxin and blocking their attachment to the enterocyte cell surface. CONCLUSIONS In conclusion, PLS has a significant antidiarrheal effect in acute and secretory diarrhea. Further investigation is needed towards its use as a natural medicine to treat diarrhea.
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Affiliation(s)
- Francisco Felipe Bezerra
- Laboratory of Proteins and Carbohydrates of Marine Algae, Department of Biochemistry and Molecular Biology - Federal University of Ceará. Fortaleza, Ceará, Brazil
| | - Glauber Cruz Lima
- Laboratory of Proteins and Carbohydrates of Marine Algae, Department of Biochemistry and Molecular Biology - Federal University of Ceará. Fortaleza, Ceará, Brazil.
| | - Nayara Alves de Sousa
- Biotechnology and Biodiversity Center Research, BIOTEC, Post-graduation program in Biotechnology - Federal University of Piauí. Parnaíba, Piauí, Brazil
| | - Willer Malta de Sousa
- Laboratory of Proteins and Carbohydrates of Marine Algae, Department of Biochemistry and Molecular Biology - Federal University of Ceará. Fortaleza, Ceará, Brazil
| | - Luís Eduardo Castanheira Costa
- Laboratory of Proteins and Carbohydrates of Marine Algae, Department of Biochemistry and Molecular Biology - Federal University of Ceará. Fortaleza, Ceará, Brazil
| | - Douglas Soares da Costa
- Biotechnology and Biodiversity Center Research, BIOTEC, Post-graduation program in Biotechnology - Federal University of Piauí. Parnaíba, Piauí, Brazil
| | - Francisco Clark Nogueira Barros
- Laboratory of Proteins and Carbohydrates of Marine Algae, Department of Biochemistry and Molecular Biology - Federal University of Ceará. Fortaleza, Ceará, Brazil; Federal Institute of Education, Science and Technology of Ceará - Juazeiro do Norte, Ceará, Brazil
| | - Jand Venes Rolim Medeiros
- Biotechnology and Biodiversity Center Research, BIOTEC, Post-graduation program in Biotechnology - Federal University of Piauí. Parnaíba, Piauí, Brazil
| | - Ana Lúcia Ponte Freitas
- Laboratory of Proteins and Carbohydrates of Marine Algae, Department of Biochemistry and Molecular Biology - Federal University of Ceará. Fortaleza, Ceará, Brazil
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12
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Dorantes-Gilardi R, Bourgeat L, Pacini L, Vuillon L, Lesieur C. In proteins, the structural responses of a position to mutation rely on the Goldilocks principle: not too many links, not too few. Phys Chem Chem Phys 2018; 20:25399-25410. [DOI: 10.1039/c8cp04530e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A disease has distinct genetic and molecular hallmarks such as sequence variants that are likely to produce the alternative protein structures accountable for individual responses to drugs and disease development.
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Affiliation(s)
| | | | - Lorenza Pacini
- Institut Rhônalpin des systèmes complexes
- IXXI-ENS-Lyon
- Lyon
- France
- AMPERE
| | - Laurent Vuillon
- LAMA
- Univ. Savoie Mont Blanc
- CNRS, LAMA
- 73376 Le Bourget du Lac
- France
| | - Claire Lesieur
- Institut Rhônalpin des systèmes complexes
- IXXI-ENS-Lyon
- Lyon
- France
- AMPERE
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13
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Serena Monaco
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
| | - Louise E. Tailford
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Jesus Angulo
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
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14
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017; 56:15289-15293. [PMID: 28977722 PMCID: PMC5725711 DOI: 10.1002/anie.201707682] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/08/2017] [Indexed: 11/21/2022]
Abstract
Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP‐STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D2O/H2O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP‐STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket.
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Affiliation(s)
- Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Louise E Tailford
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
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15
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Heggelund JE, Mackenzie A, Martinsen T, Heim JB, Cheshev P, Bernardi A, Krengel U. Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics. Sci Rep 2017; 7:2326. [PMID: 28539625 PMCID: PMC5443773 DOI: 10.1038/s41598-017-02179-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/07/2017] [Indexed: 01/08/2023] Open
Abstract
Cholera is a life-threatening disease in many countries, and new drugs are clearly needed. C-glycosidic antagonists may serve such a purpose. Here we report atomic-resolution crystal structures of three such compounds in complexes with the cholera toxin. The structures give unprecedented atomic details of the molecular interactions and show how the inhibitors efficiently block the GM1 binding site. These molecules are well suited for development into low-cost prophylactic drugs, due to their relatively easy synthesis and their resistance to glycolytic enzymes. One of the compounds links two toxin B-pentamers in the crystal structure, which may yield improved inhibition through the formation of toxin aggregates. These structures can spark the improved design of GM1 mimics, either alone or as multivalent inhibitors connecting multiple GM1-binding sites. Future developments may further include compounds that link the primary and secondary binding sites. Serving as decoys, receptor mimics may lessen symptoms while avoiding the use of antibiotics.
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Affiliation(s)
- Julie Elisabeth Heggelund
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway. .,School of Biomedical Sciences, University of Leeds, LS2 9JT Leeds, UK and School of Pharmacy, University of Oslo, P.O. Box 1068, NO-0316, Blindern, Norway.
| | - Alasdair Mackenzie
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway.,Alere Technologies AS, Kjelsåsveien 161, NO-0884, Oslo, Norway
| | - Tobias Martinsen
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway
| | - Joel Benjamin Heim
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway
| | - Pavel Cheshev
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, 20133, Milano, Italy.,Skolkovo innovation center, Office 229, OC Technopark bld. 2, Lugovaya str. 4, 143026, Moscow, Russia
| | - Anna Bernardi
- Universita' degli Studi di Milano, Dipartimento di Chimica, via Golgi 19, 20133, Milano, Italy
| | - Ute Krengel
- Department of Chemistry, University of Oslo, P.O. Box 1033, NO-0315, Blindern, Norway.
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16
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Affiliation(s)
- Megan Garland
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Sebastian Loscher
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
| | - Matthew Bogyo
- Cancer
Biology Program, ‡Department of Pathology, §Department of Microbiology and Immunology, and ∥Department of
Chemical and Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, United States
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17
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Quantitative Proteomic Analysis of Escherichia coli Heat-Labile Toxin B Subunit (LTB) with Enterovirus 71 (EV71) Subunit VP1. Int J Mol Sci 2016; 17:ijms17091419. [PMID: 27618897 PMCID: PMC5037698 DOI: 10.3390/ijms17091419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 02/06/2023] Open
Abstract
The nontoxic heat-labile toxin (LT) B subunit (LTB) was used as mucosal adjuvant experimentally. However, the mechanism of LTB adjuvant was still unclear. The LTB and enterovirus 71 (EV71) VP1 subunit (EVP1) were constructed in pET32 and expressed in E. coli BL21, respectively. The immunogenicity of purified EVP1 and the adjuvanticity of LTB were evaluated via intranasal immunization EVP1 plus LTB in Balb/c mice. In order to elucidate the proteome change triggered by the adjuvant of LTB, the proteomic profiles of LTB, EVP1, and LTB plus EVP1 were quantitatively analyzed by iTRAQ-LC-MS/MS (isobaric tags for relative and absolute quantitation; liquid chromatography-tandem mass spectrometry) in murine macrophage RAW264.7. The proteomic data were analyzed by bioinformatics and validated by western blot analysis. The predicted protein interactions were confirmed using LTB pull-down and the LTB processing pathway was validated by confocal microscopy. The results showed that LTB significantly boosted EVP1 specific systematic and mucosal antibodies. A total of 3666 differential proteins were identified in the three groups. Pathway enrichment of proteomic data predicted that LTB upregulated the specific and dominant MAPK (mitogen-activated protein kinase) signaling pathway and the protein processing in endoplasmic reticulum (PPER) pathway, whereas LTB or EVP1 did not significantly upregulate these two signaling pathways. Confocal microscopy and LTB pull-down assays confirmed that the LTB adjuvant was endocytosed and processed through endocytosis (ENS)-lysosomal-endoplasmic reticulum (ER) system.
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18
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Badshah SL, Khan AN, Mabkhot YN. Molecular Dynamics Simulation of Cholera Toxin A-1 Polypeptide. OPEN CHEM 2016. [DOI: 10.1515/chem-2016-0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
AbstractA molecular dynamics (MD) simulation study of the enzymatic portion of cholera toxin; cholera toxin A-1 polypeptide (CTA1) was performed at 283, 310 and 323 K. From total energy analysis it was observed that this toxin is stable thermodynamically and these outcomes were likewise confirmed by root mean square deviations (RMSD) investigations. The Cα root mean square fluctuation (RMSF) examinations revealed that there are a number of residues inside CTA1, which can be used as target for designing and synthesizing inhibitory drugs, in order to inactivate cholera toxin inside the human body. The fluctuations in the radius of gyration and hydrogen bonding in CTA1 proved that protein unfolding and refolding were normal routine phenomena in its structure at all temperatures. Solvent accessible surface area study identified the hydrophilic nature of the CTA1, and due to this property it can be a potential biological weapon. The structural identification (STRIDE) algorithm for proteins was successfully used to determine the partially disordered secondary structure of CTA1. On account of this partially disordered secondary structure, it can easily deceive the proteolytic enzymes of the endoplasmic reticulum of host cells.
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Affiliation(s)
- Syed Lal Badshah
- 1National Center of Excellence in Physical Chemistry, University of Peshawar, Khyber Pukhtoonkhwa, Pakistan. 25120
- 2Department Biochemistry, Abdul Wali Khan University Mardan. Khyber Pukhtoonkhwa, Pakistan
- 3Department of Chemistry, Islamia College University Peshawar, Peshawar, Khyber Pukhtoonkhwa, Pakistan. 25120
| | - Abdul Naeem Khan
- 1National Center of Excellence in Physical Chemistry, University of Peshawar, Khyber Pukhtoonkhwa, Pakistan. 25120
- 2Department Biochemistry, Abdul Wali Khan University Mardan. Khyber Pukhtoonkhwa, Pakistan
| | - Yahia Nasser Mabkhot
- 3Department of Chemistry, Islamia College University Peshawar, Peshawar, Khyber Pukhtoonkhwa, Pakistan. 25120
- 4Department of Chemistry, College of Sciences, King Saud University, Riyadh 11451. Saudi Arabia
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19
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Cody V, Pace J, Nawar HF, King-Lyons N, Liang S, Connell TD, Hajishengallis G. Structure-activity correlations of variant forms of the B pentamer of Escherichia coli type II heat-labile enterotoxin LT-IIb with Toll-like receptor 2 binding. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1604-12. [PMID: 23151625 PMCID: PMC3498930 DOI: 10.1107/s0907444912038917] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/11/2012] [Indexed: 03/21/2023]
Abstract
The pentameric B subunit of the type II heat-labile enterotoxin of Escherichia coli (LT-IIb-B(5)) is a potent signaling molecule capable of modulating innate immune responses. It has previously been shown that LT-IIb-B(5), but not the LT-IIb-B(5) Ser74Asp variant [LT-IIb-B(5)(S74D)], activates Toll-like receptor (TLR2) signaling in macrophages. Consistent with this, the LT-IIb-B(5)(S74D) variant failed to bind TLR2, in contrast to LT-IIb-B(5) and the LT-IIb-B(5) Thr13Ile [LT-IIb-B(5)(T13I)] and LT-IIb-B(5) Ser74Ala [LT-IIb-B(5)(S74A)] variants, which displayed the highest binding activity to TLR2. Crystal structures of the Ser74Asp, Ser74Ala and Thr13Ile variants of LT-IIb-B(5) have been determined to 1.90, 1.40 and 1.90 Å resolution, respectively. The structural data for the Ser74Asp variant reveal that the carboxylate side chain points into the pore, thereby reducing the pore size compared with that of the wild-type or the Ser74Ala variant B pentamer. On the basis of these crystallographic data, the reduced TLR2-binding affinity of the LT-IIb-B(5)(S74D) variant may be the result of the pore of the pentamer being closed. On the other hand, the explanation for the enhanced TLR2-binding activity of the LT-IIb-B(5)(S74A) variant is more complex as its activity is greater than that of the wild-type B pentamer, which also has an open pore as the Ser74 side chain points away from the pore opening. Data for the LT-IIb-B(5)(T13I) variant show that four of the five variant side chains point to the outside surface of the pentamer and one residue points inside. These data are consistent with the lack of binding of the LT-IIb-B(5)(T13I) variant to GD1a ganglioside.
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Affiliation(s)
- Vivian Cody
- Structural Biology Department, Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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20
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Tran HA, Kitov PI, Paszkiewicz E, Sadowska JM, Bundle DR. Multifunctional multivalency: a focused library of polymeric cholera toxin antagonists. Org Biomol Chem 2011; 9:3658-71. [PMID: 21451844 DOI: 10.1039/c0ob01089h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Structural pre-organization of the multivalent ligands is important for successful interaction with multimeric proteins. Polymer-based heterobifunctional ligands that contain pendant groups prearranged into heterodimers can be used to probe the active site and surrounding area of the receptor. Here we describe the synthesis and activities of a series of galactose conjugates on polyacrylamide and dextran. Conjugation of a second fragment resulted in nanomolar inhibitors of cholera toxin, while the galactose-only progenitors showed no detectable activity.
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Affiliation(s)
- Huu-Anh Tran
- Alberta Ingenuity Centre for Carbohydrate Science, Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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21
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Holmner A, Mackenzie A, Okvist M, Jansson L, Lebens M, Teneberg S, Krengel U. Crystal structures exploring the origins of the broader specificity of escherichia coli heat-labile enterotoxin compared to cholera toxin. J Mol Biol 2010; 406:387-402. [PMID: 21168418 DOI: 10.1016/j.jmb.2010.11.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/26/2010] [Accepted: 11/30/2010] [Indexed: 11/28/2022]
Abstract
Cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) are structurally and functionally related and share the same primary receptor, the GM1 ganglioside. Despite their extensive similarities, these two toxins exhibit distinct ligand specificities, with LT being more promiscuous than CT. Here, we have attempted to rationalize the broader binding specificity of LT and the subtle differences between the binding characteristics of LTs from human and porcine origins (mediated by their B subunit pentamers, hLTB and pLTB, respectively). The analysis is based on two crystal structures of pLTB in complexes with the pentasaccharide of its primary ligand, GM1, and with neolactotetraose, the carbohydrate determinant of a typical secondary ligand of LTs, respectively. Important molecular determinants underlying the different binding specificities of LTB and CTB are found to be contributed by Ser95, Tyr18 and Thr4 (or Ser4 of hLTB), which together prestabilize the binding site by positioning Lys91, Glu51 and the adjacent loop region (50-61) containing Ile58 for ligand binding. Glu7 and Ala1 may also play an important role. Many of these residues are closely connected with a recently identified second binding site, and there appears to be cross-talk between the two sites. Binding to N-acetyllactosamine-terminated receptors is further augmented by Arg13 (present in pLT and some hLT variants), as previously predicted.
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Affiliation(s)
- Asa Holmner
- Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, NO-0315 Oslo, Norway.
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22
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Analysis of a cholera toxin B subunit (CTB) and human mucin 1 (MUC1) conjugate protein in a MUC1-tolerant mouse model. Cancer Immunol Immunother 2010; 59:1801-11. [PMID: 20824430 DOI: 10.1007/s00262-010-0906-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 08/06/2010] [Indexed: 10/19/2022]
Abstract
Since epithelial mucin 1 (MUC1) is associated with several adenocarcinomas at the mucosal sites, it is pertinent to test the efficacy of a mucosally targeted vaccine formulation. The B subunit of the Vibrio cholerae cholera toxin (CTB) has great potential to act as a mucosal carrier for subunit vaccines. In the present study we evaluated whether a MUC1 tandem repeat (TR) peptide chemically linked to CTB would break self-antigen tolerance in the transgenic MUC1-tolerant mouse model (MUC1.Tg) through oral or parenteral immunizations. We report that oral immunization with the CTB-MUC1 conjugate along with mucosal adjuvant, unmethylated CpG oligodeoxynucleotide (ODN) and interleukin-12 (IL-12) did not break self-antigen tolerance in MUC1.Tg mice, but induced a strong humoral response in wild-type C57BL/6 mice. However, self-antigen tolerance in the MUC1.Tg mouse model was broken after parenteral immunizations with different doses of the CTB-MUC1 conjugate protein and with the adjuvant CpG ODN co-delivered with CTB-MUC1. Importantly, mice immunized systemically with CpG ODN alone and with CTB-MUC1 exhibited decreased tumor burden when challenged with a mammary gland tumor cell line that expresses human MUC1.
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23
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Mudrak B, Kuehn MJ. Heat-labile enterotoxin: beyond G(m1) binding. Toxins (Basel) 2010; 2:1445-70. [PMID: 22069646 PMCID: PMC3153253 DOI: 10.3390/toxins2061445] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 05/22/2010] [Accepted: 06/07/2010] [Indexed: 01/07/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a significant source of morbidity and mortality worldwide. One major virulence factor released by ETEC is the heat-labile enterotoxin LT, which is structurally and functionally similar to cholera toxin. LT consists of five B subunits carrying a single catalytically active A subunit. LTB binds the monosialoganglioside GM1, the toxin’s host receptor, but interactions with A-type blood sugars and E. coli lipopolysaccharide have also been identified within the past decade. Here, we review the regulation, assembly, and binding properties of the LT B-subunit pentamer and discuss the possible roles of its numerous molecular interactions.
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Affiliation(s)
- Benjamin Mudrak
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Meta J. Kuehn
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-919-684-2545; Fax: +1-919-684-8885
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24
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Chen JC, Ho TY, Chang YS, Wu SL, Li CC, Hsiang CY. Identification of Escherichia coli enterotoxin inhibitors from traditional medicinal herbs by in silico, in vitro, and in vivo analyses. JOURNAL OF ETHNOPHARMACOLOGY 2009; 121:372-378. [PMID: 19063958 DOI: 10.1016/j.jep.2008.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Revised: 11/03/2008] [Accepted: 11/08/2008] [Indexed: 05/27/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Glycyrrhiza uralensis has been used for the treatment of gastrointestinal disorders, such as diarrhea, in several ancient cultures. Glycyrrhizin is the principal component of liquorice and lots of pharmacological effects have been demonstrated. AIM OF THE STUDY Heat-labile enterotoxin (LT), the virulence factor of enterotoxigenic Escherichia coli, induces diarrhea by initially binding to the GM1 on the surfaces of intestinal epithelial cells and consequently leading to the massive loss of fluid and ions from cells. Therefore, we evaluated the inhibitory effects of traditional medicinal herbs (TMH) on the B subunit of LT (LTB) and GM1 interaction. MATERIALS AND METHODS The inhibitory effects of TMH on LTB-GM1 interaction were evaluated by GM1-enzyme-linked immunosorbent assay (ELISA). The likely active phytochemicals of these TMH were then predicted by in silico model (docking) and analyzed by in vitro (GM1-ELISA) and in vivo (patent mouse gut assay) models. RESULTS We found that various TMH, which have been ethnomedically used for the treatment of diarrhea, inhibited the LTB-GM1 interaction. Docking data showed that triterpenoids were the most active phytochemicals and the oleanane-type triterpenoids presented better LTB-binding abilities than other types of triterpenoids. Moreover, by in vitro and in vivo models, we demonstrated that glycyrrhizin was the most effective oleanane-type triterpenoid that significantly suppressed both the LTB-binding ability (IC50=3.26+/-0.17 mM) and the LT-induced fluid accumulation in mice. CONCLUSIONS We found an LT inhibitor, glycyrrhizin, from TMH by in silico, in vitro, and in vivo analyses.
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Affiliation(s)
- Jaw-Chyun Chen
- Graduate Institute of Chinese Pharmaceutical Sciences, China Medical University, Taichung, Taiwan
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25
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Hill AD, Reilly PJ. A Gibbs free energy correlation for automated docking of carbohydrates. J Comput Chem 2008; 29:1131-41. [PMID: 18074341 DOI: 10.1002/jcc.20873] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large binding data set has been assembled from the literature. The data set contains information from 262 unique protein-carbohydrate crystal structures for which experimental binding information is known. Hydrogen atoms were added to the structures and training conformations were generated with the automated docking program AutoDock 3.06, resulting in a training set of 225,920 all-atom conformations. In all, 288 formulations of the AutoDock 3.0 free energy model were trained against the data set, testing each of four alternate methods of computing the van der Waals, solvation, and hydrogen-bonding energetic components. The van der Waals parameters from AutoDock 1 produced the lowest errors, and an entropic model derived from statistical mechanics produced the only models with five physically and statistically significant coefficients. Eight models predict the Gibbs free energy of binding with an error of less than 40% of the error of any similar models previously published.
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Affiliation(s)
- Anthony D Hill
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
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26
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Blais DR, Altosaar I. Humanizing infant milk formula to decrease postnatal HIV transmission. Trends Biotechnol 2007; 25:376-84. [PMID: 17659799 DOI: 10.1016/j.tibtech.2007.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 05/21/2007] [Accepted: 07/18/2007] [Indexed: 01/03/2023]
Abstract
There are currently no safe methods for feeding babies born from the 16 million HIV-infected women living in resource-constrained countries. Breast milk can transmit HIV, and formula feeding can lead to gastrointestinal illnesses owing to unsanitary conditions and the composition of milk formulations. There is therefore a need to ensure that breast milk substitutes provide optimal health outcomes. Given that the immune properties of several breast milk proteins are known, transgenic food crops could facilitate inexpensive and safe reconstitution of the beneficial breast milk proteome in infant formulae, while keeping the HIV virus at bay. At least seven breast milk immune proteins have already been produced in food crops, and dozens more proteins could potentially be produced if fortified formula proves effective in nursing newborns born to HIV-infected mothers.
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Affiliation(s)
- David R Blais
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
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27
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Ghatnekar-Nilsson S, Dexlin L, Wingren C, Montelius L, Borrebaeck CAK. Design of atto-vial based recombinant antibody arrays combined with a planar wave-guide detection system. Proteomics 2007; 7:540-547. [PMID: 17309099 DOI: 10.1002/pmic.200600485] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Antibody microarray is a rapidly emerging, powerful approach with great promise within high-throughput proteomics. However, before a truly proteome-wide analysis can be performed, the antibody array format needs to be miniaturized even further in order to enable ultradense arrays to be fabricated. To this end, we have designed and generated proof-of-concept for the first generation of an atto-vial based recombinant antibody array platform. Briefly, we have designed a novel nanostructured substrate using electron beam lithography. Vials, ranging in volume/size from 6 (200 nm in diameter) to 4000 aL (5 microm in diameter), were fabricated. Human recombinant single-chain Fv antibody fragments, microarray adopted by design, were used as probes. The set-up was interfaced with planar wave-guide technology for evanescant field fluorescence detection. The results showed that protein analytes could be specifically detected in the subzeptomole range for pure systems, using vials down to 57 aL. Further, low-abundant (pg/mL) protein analytes could be detected in directly labeled complex proteomes, such as human whole serum, using 157 aL-vials. Taken together, these results outline the potential of the atto-vial array set-up for miniaturized affinity proteomics-based approaches.
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Affiliation(s)
- Sara Ghatnekar-Nilsson
- Department of Solid State Physics, The Nanometer Structure Consortium, Lund University, Lund, Sweden
| | - Linda Dexlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Lars Montelius
- Department of Solid State Physics, The Nanometer Structure Consortium, Lund University, Lund, Sweden
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28
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Abstract
Delivery of vaccines to mucosal surfaces can elicit humoral and cell-mediated responses of the mucosal and systemic immune systems, evoke less pain and discomfort than parenteral delivery, and eliminate needle-associated risks. Transgenic plants are an ideal means by which to produce oral vaccines, as the rigid walls of the plant cell protect antigenic proteins from the acidic environment of the stomach, enabling intact antigen to reach the gut associated lymphoid tissue. In the past few years, new techniques (such as chloroplast transformation and food processing) have improved antigen concentration in transgenic plants. In addition, adjuvants and targeting proteins have increased the immunogenicity of mucosally administered plant-made vaccines. These studies have moved plant-made vaccines closer to the development phase.
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MESH Headings
- Administration, Oral
- Animals
- Chlamydomonas reinhardtii/cytology
- Chlamydomonas reinhardtii/genetics
- Chlamydomonas reinhardtii/metabolism
- Gene Expression/genetics
- Humans
- Immunity, Mucosal/immunology
- Legislation, Drug
- Mice
- Plant Structures/genetics
- Plant Structures/growth & development
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Tissue Culture Techniques
- Nicotiana/cytology
- Nicotiana/genetics
- Nicotiana/metabolism
- Vaccines, Edible/administration & dosage
- Vaccines, Edible/biosynthesis
- Vaccines, Edible/immunology
- Vaccines, Subunit/administration & dosage
- Vaccines, Subunit/biosynthesis
- Vaccines, Subunit/immunology
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/biosynthesis
- Vaccines, Synthetic/immunology
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Affiliation(s)
- M Manuela Rigano
- The Biodesign Institute at Arizona State University, School of Life Sciences, Arizona State University, Tempe, 85287, USA
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29
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Holmner A, Lebens M, Teneberg S, Angström J, Okvist M, Krengel U. Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin: 1.9 A crystal structure reveals the details. Structure 2005; 12:1655-67. [PMID: 15341730 DOI: 10.1016/j.str.2004.06.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2004] [Revised: 06/10/2004] [Accepted: 06/24/2004] [Indexed: 10/26/2022]
Abstract
A hybrid between the B subunits of cholera toxin and Escherichia coli heat-labile enterotoxin has been described, which exhibits a novel binding specificity to blood group A and B type 2 determinants. In the present investigation, we have determined the crystal structure of this protein hybrid, termed LCTBK, in complex with the blood group A pentasaccharide GalNAcalpha3(Fucalpha2)Galbeta4(Fucalpha3)GlcNAcbeta, confirming not only the novel binding specificity but also a distinct new oligosaccharide binding site. Binding studies revealed that the new specificity can be ascribed to a single mutation (S4N) introduced into the sequence of Escherichia coli heat-labile enterotoxin. At a resolution of 1.9 A, the new binding site is resolved in excellent detail. Main features include a complex network of water molecules, which is well preserved by the parent toxins, and an unexpectedly modest contribution to binding by the critical residue Asn4, which interacts with the ligand only via a single water molecule.
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Affiliation(s)
- Asa Holmner
- Department of Chemistry and Bioscience, Chalmers University of Technology, PO Box 462, SE-40530 Göteborg, Sweden.
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30
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Golubev AM, Nagem RAP, Brandão Neto JR, Neustroev KN, Eneyskaya EV, Kulminskaya AA, Shabalin KA, Savel'ev AN, Polikarpov I. Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism. J Mol Biol 2004; 339:413-22. [PMID: 15136043 DOI: 10.1016/j.jmb.2004.03.062] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 03/15/2004] [Accepted: 03/23/2004] [Indexed: 11/18/2022]
Abstract
The crystal structures of alpha-galactosidase from the mesophilic fungus Trichoderma reesei and its complex with the competitive inhibitor, beta-d-galactose, have been determined at 1.54 A and 2.0 A resolution, respectively. The alpha-galactosidase structure was solved by the quick cryo-soaking method using a single Cs derivative. The refined crystallographic model of the alpha-galactosidase consists of two domains, an N-terminal catalytic domain of the (beta/alpha)8 barrel topology and a C-terminal domain which is formed by an antiparallel beta-structure. The protein contains four N-glycosylation sites located in the catalytic domain. Some of the oligosaccharides were found to participate in inter-domain contacts. The galactose molecule binds to the active site pocket located in the center of the barrel of the catalytic domain. Analysis of the alpha-galactosidase- galactose complex reveals the residues of the active site and offers a structural basis for identification of the putative mechanism of the enzymatic reaction. The structure of the alpha-galactosidase closely resembles those of the glycoside hydrolase family 27. The conservation of two catalytic Asp residues, identified for this family, is consistent with a double-displacement reaction mechanism for the alpha-galactosidase. Modeling of possible substrates into the active site reveals specific hydrogen bonds and hydrophobic interactions that could explain peculiarities of the enzyme kinetics.
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Affiliation(s)
- A M Golubev
- Petersburg Nuclear Physics Institute, Gatchina, St Petersburg, 188300, Russia
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31
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Zavala-Ruiz Z, Sundberg EJ, Stone JD, DeOliveira DB, Chan IC, Svendsen J, Mariuzza RA, Stern LJ. Exploration of the P6/P7 region of the peptide-binding site of the human class II major histocompatability complex protein HLA-DR1. J Biol Chem 2003; 278:44904-12. [PMID: 12952957 DOI: 10.1074/jbc.m307652200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of the class II major histocompatibilty complex (MHC) protein, HLA-DR1, generally show a tight fit between MHC and bound peptide except in the P6/P7 region of the peptide-binding site. In this region, there is a shallow water-filled pocket underneath the peptide and between the pockets that accommodate the P6 and P7 side chains. We investigated the properties of this pocket with the idea of engineering substitutions into the corresponding region of peptide antigens to increase their binding affinity for HLA-DR1. We investigated d-amino acids and N-alkyl modifications at both the P6 and P7 positions of the peptide and found that binding of peptides to HLA-DR1 could be increased by incorporating an N-methyl substitution at position 7 of the peptide. The crystal structure of HLA-DR1 bound to a peptide containing a P7 N-methyl alanine was determined. The N-methyl group orients in the P6/P7 pocket, displacing one of the waters usually bound in this pocket. The structure shows that the substitution does not alter the conformation of the bound peptide, which adopts the usual polyproline type II helix. An antigenic peptide carrying the N-methyl modification is taken up by antigen-presenting cells and loaded onto endogenous class II MHC molecules for presentation, and the resultant MHC-peptide complexes activate antigen-specific T-cells. These results suggest a possible strategy for increasing the affinity of weakly immunogenic peptides that might be applicable to the development of vaccines and diagnostic reagents.
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Affiliation(s)
- Zarixia Zavala-Ruiz
- Massachusetts Institute of Technology, Department of Chemistry, Cambridge, Massachusetts 02139, USA
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